1
|
Gupta P, Geniza M, Elser J, Al-Bader N, Baschieri R, Phillips JL, Haq E, Preece J, Naithani S, Jaiswal P. Reference genome of the nutrition-rich orphan crop chia ( Salvia hispanica) and its implications for future breeding. Front Plant Sci 2023; 14:1272966. [PMID: 38162307 PMCID: PMC10757625 DOI: 10.3389/fpls.2023.1272966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Chia (Salvia hispanica L.) is one of the most popular nutrition-rich foods and pseudocereal crops of the family Lamiaceae. Chia seeds are a rich source of proteins, polyunsaturated fatty acids (PUFAs), dietary fibers, and antioxidants. In this study, we present the assembly of the chia reference genome, which spans 303.6 Mb and encodes 48,090 annotated protein-coding genes. Our analysis revealed that ~42% of the chia genome harbors repetitive content, and identified ~3 million single nucleotide polymorphisms (SNPs) and 15,380 simple sequence repeat (SSR) marker sites. By investigating the chia transcriptome, we discovered that ~44% of the genes undergo alternative splicing with a higher frequency of intron retention events. Additionally, we identified chia genes associated with important nutrient content and quality traits, such as the biosynthesis of PUFAs and seed mucilage fiber (dietary fiber) polysaccharides. Notably, this is the first report of in-silico annotation of a plant genome for protein-derived small bioactive peptides (biopeptides) associated with improving human health. To facilitate further research and translational applications of this valuable orphan crop, we have developed the Salvia genomics database (SalviaGDB), accessible at https://salviagdb.org.
Collapse
Affiliation(s)
- Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Noor Al-Bader
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Rachel Baschieri
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeremy Levi Phillips
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Ebaad Haq
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| |
Collapse
|
2
|
Kouli O, Murray V, Bhatia S, Cambridge WA, Kawka M, Shafi S, Knight SR, Kamarajah SK, McLean KA, Glasbey JC, Khaw RA, Ahmed W, Akhbari M, Baker D, Borakati A, Mills E, Thavayogan R, Yasin I, Raubenheimer K, Ridley W, Sarrami M, Zhang G, Egoroff N, Pockney P, Richards T, Bhangu A, Creagh-Brown B, Edwards M, Harrison EM, Lee M, Nepogodiev D, Pinkney T, Pearse R, Smart N, Vohra R, Sohrabi C, Jamieson A, Nguyen M, Rahman A, English C, Tincknell L, Kakodkar P, Kwek I, Punjabi N, Burns J, Varghese S, Erotocritou M, McGuckin S, Vayalapra S, Dominguez E, Moneim J, Salehi M, Tan HL, Yoong A, Zhu L, Seale B, Nowinka Z, Patel N, Chrisp B, Harris J, Maleyko I, Muneeb F, Gough M, James CE, Skan O, Chowdhury A, Rebuffa N, Khan H, Down B, Fatimah Hussain Q, Adams M, Bailey A, Cullen G, Fu YXJ, McClement B, Taylor A, Aitken S, Bachelet B, Brousse de Gersigny J, Chang C, Khehra B, Lahoud N, Lee Solano M, Louca M, Rozenbroek P, Rozitis E, Agbinya N, Anderson E, Arwi G, Barry I, Batchelor C, Chong T, Choo LY, Clark L, Daniels M, Goh J, Handa A, Hanna J, Huynh L, Jeon A, Kanbour A, Lee A, Lee J, Lee T, Leigh J, Ly D, McGregor F, Moss J, Nejatian M, O'Loughlin E, Ramos I, Sanchez B, Shrivathsa A, Sincari A, Sobhi S, Swart R, Trimboli J, Wignall P, Bourke E, Chong A, Clayton S, Dawson A, Hardy E, Iqbal R, Le L, Mao S, Marinelli I, Metcalfe H, Panicker D, R HH, Ridgway S, Tan HH, Thong S, Van M, Woon S, Woon-Shoo-Tong XS, Yu S, Ali K, Chee J, Chiu C, Chow YW, Duller A, Nagappan P, Ng S, Selvanathan M, Sheridan C, Temple M, Do JE, Dudi-Venkata NN, Humphries E, Li L, Mansour LT, Massy-Westropp C, Fang B, Farbood K, Hong H, Huang Y, Joan M, Koh C, Liu YHA, Mahajan T, Muller E, Park R, Tanudisastro M, Wu JJG, Chopra P, Giang S, Radcliffe S, Thach P, Wallace D, Wilkes A, Chinta SH, Li J, Phan J, Rahman F, Segaran A, Shannon J, Zhang M, Adams N, Bonte A, Choudhry A, Colterjohn N, Croyle JA, Donohue J, Feighery A, Keane A, McNamara D, Munir K, Roche D, Sabnani R, Seligman D, Sharma S, Stickney Z, Suchy H, Tan R, Yordi S, Ahmed I, Aranha M, El Sabawy D, Garwood P, Harnett M, Holohan R, Howard R, Kayyal Y, Krakoski N, Lupo M, McGilberry W, Nepon H, Scoleri Y, Urbina C, Ahmad Fuad MF, Ahmed O, Jaswantlal D, Kelly E, Khan MHT, Naidu D, Neo WX, O'Neill R, Sugrue M, Abbas JD, Abdul-Fattah S, Azlan A, Barry K, Idris NS, Kaka N, Mc Dermott D, Mohammad Nasir MN, Mozo M, Rehal A, Shaikh Yousef M, Wong RH, Curran E, Gardner M, Hogan A, Julka R, Lasser G, Ní Chorráin N, Ting J, Browne R, George S, Janjua Z, Leung Shing V, Megally M, Murphy S, Ravenscroft L, Vedadi A, Vyas V, Bryan A, Sheikh A, Ubhi J, Vannelli K, Vawda A, Adeusi L, Doherty C, Fitzgerald C, Gallagher H, Gill P, Hamza H, Hogan M, Kelly S, Larry J, Lynch P, Mazeni NA, O'Connell R, O'Loghlin R, Singh K, Abbas Syed R, Ali A, Alkandari B, Arnold A, Arora E, Azam R, Breathnach C, Cheema J, Compton M, Curran S, Elliott JA, Jayasamraj O, Mohammed N, Noone A, Pal A, Pandey S, Quinn P, Sheridan R, Siew L, Tan EP, Tio SW, Toh VTR, Walsh M, Yap C, Yassa J, Young T, Agarwal N, Almoosawy SA, Bowen K, Bruce D, Connachan R, Cook A, Daniell A, Elliott M, Fung HKF, Irving A, Laurie S, Lee YJ, Lim ZX, Maddineni S, McClenaghan RE, Muthuganesan V, Ravichandran P, Roberts N, Shaji S, Solt S, Toshney E, Arnold C, Baker O, Belais F, Bojanic C, Byrne M, Chau CYC, De Soysa S, Eldridge M, Fairey M, Fearnhead N, Guéroult A, Ho JSY, Joshi K, Kadiyala N, Khalid S, Khan F, Kumar K, Lewis E, Magee J, Manetta-Jones D, Mann S, McKeown L, Mitrofan C, Mohamed T, Monnickendam A, Ng AYKC, Ortu A, Patel M, Pope T, Pressling S, Purohit K, Saji S, Shah Foridi J, Shah R, Siddiqui SS, Surman K, Utukuri M, Varghese A, Williams CYK, Yang JJ, Billson E, Cheah E, Holmes P, Hussain S, Murdock D, Nicholls A, Patel P, Ramana G, Saleki M, Spence H, Thomas D, Yu C, Abousamra M, Brown C, Conti I, Donnelly A, Durand M, French N, Goan R, O'Kane E, Rubinchik P, Gardiner H, Kempf B, Lai YL, Matthews H, Minford E, Rafferty C, Reid C, Sheridan N, Al Bahri T, Bhoombla N, Rao BM, Titu L, Chatha S, Field C, Gandhi T, Gulati R, Jha R, Jones Sam MT, Karim S, Patel R, Saunders M, Sharma K, Abid S, Heath E, Kurup D, Patel A, Ali M, Cresswell B, Felstead D, Jennings K, Kaluarachchi T, Lazzereschi L, Mayson H, Miah JE, Reinders B, Rosser A, Thomas C, Williams H, Al-Hamid Z, Alsadoun L, Chlubek M, Fernando P, Gaunt E, Gercek Y, Maniar R, Ma R, Matson M, Moore S, Morris A, Nagappan PG, Ratnayake M, Rockall L, Shallcross O, Sinha A, Tan KE, Virdee S, Wenlock R, Donnelly HA, Ghazal R, Hughes I, Liu X, McFadden M, Misbert E, Mogey P, O'Hara A, Peace C, Rainey C, Raja P, Salem M, Salmon J, Tan CH, Alves D, Bahl S, Baker C, Coulthurst J, Koysombat K, Linn T, Rai P, Sharma A, Shergill A, Ahmed M, Ahmed S, Belk LH, Choudhry H, Cummings D, Dixon Y, Dobinson C, Edwards J, Flint J, Franco Da Silva C, Gallie R, Gardener M, Glover T, Greasley M, Hatab A, Howells R, Hussey T, Khan A, Mann A, Morrison H, Ng A, Osmond R, Padmakumar N, Pervaiz F, Prince R, Qureshi A, Sawhney R, Sigurdson B, Stephenson L, Vora K, Zacken A, Cope P, Di Traglia R, Ferarrio I, Hackett N, Healicon R, Horseman L, Lam LI, Meerdink M, Menham D, Murphy R, Nimmo I, Ramaesh A, Rees J, Soame R, Dilaver N, Adebambo D, Brown E, Burt J, Foster K, Kaliyappan L, Knight P, Politis A, Richardson E, Townsend J, Abdi M, Ball M, Easby S, Gill N, Ho E, Iqbal H, Matthews M, Nubi S, Nwokocha JO, Okafor I, Perry G, Sinartio B, Vanukuru N, Walkley D, Welch T, Yates J, Yeshitila N, Bryans K, Campbell B, Gray C, Keys R, Macartney M, Chamberlain G, Khatri A, Kucheria A, Lee STP, Reese G, Roy choudhury J, Tan WYR, Teh JJ, Ting A, Kazi S, Kontovounisios C, Vutipongsatorn K, Amarnath T, Balasubramanian N, Bassett E, Gurung P, Lim J, Panjikkaran A, Sanalla A, Alkoot M, Bacigalupo V, Eardley N, Horton M, Hurry A, Isti C, Maskell P, Nursiah K, Punn G, Salih H, Epanomeritakis E, Foulkes A, Henderson R, Johnston E, McCullough H, McLarnon M, Morrison E, Cheung A, Cho SH, Eriksson F, Hedges J, Low Z, May C, Musto L, Nagi S, Nur S, Salau E, Shabbir S, Thomas MC, Uthayanan L, Vig S, Zaheer M, Zeng G, Ashcroft-Quinn S, Brown R, Hayes J, McConville R, French R, Gilliam A, Sheetal S, Shehzad MU, Bani W, Christie I, Franklyn J, Khan M, Russell J, Smolarek S, Varadarassou R, Ahmed SK, Narayanaswamy S, Sealy J, Shah M, Dodhia V, Manukyan A, O'Hare R, Orbell J, Chung I, Forenc K, Gupta A, Agarwal A, Al Dabbagh A, Bennewith R, Bottomley J, Chu TSM, Chu YYA, Doherty W, Evans B, Hainsworth P, Hosfield T, Li CH, McCullagh I, Mehta A, Thaker A, Thompson B, Virdi A, Walker H, Wilkins E, Dixon C, Hassan MR, Lotca N, Tong KS, Batchelor-Parry H, Chaudhari S, Harris T, Hooper J, Johnson C, Mulvihill C, Nayler J, Olutobi O, Piramanayagam B, Stones K, Sussman M, Weaver C, Alam F, Al Rawi M, Andrew F, Arrayeh A, Azizan N, Hassan A, Iqbal Z, John I, Jones M, Kalake O, Keast M, Nicholas J, Patil A, Powell K, Roberts P, Sabri A, Segue AK, Shah A, Shaik Mohamed SA, Shehadeh A, Shenoy S, Tong A, Upcott M, Vijayasingam D, Anarfi S, Dauncey J, Devindaran A, Havalda P, Komninos G, Mwendwa E, Norman C, Richards J, Urquhart A, Allan J, Cahya E, Hunt H, McWhirter C, Norton R, Roxburgh C, Tan JY, Ali Butt S, Hansdot S, Haq I, Mootien A, Sanchez I, Vainas T, Deliyannis E, Tan M, Vipond M, Chittoor Satish NN, Dattani A, De Carvalho L, Gaston-Grubb M, Karunanithy L, Lowe B, Pace C, Raju K, Roope J, Taylor C, Youssef H, Munro T, Thorn C, Wong KHF, Yunus A, Chawla S, Datta A, Dinesh AA, Field D, Georgi T, Gwozdz A, Hamstead E, Howard N, Isleyen N, Jackson N, Kingdon J, Sagoo KS, Schizas A, Yin L, Aung E, Aung YY, Franklin S, Han SM, Kim WC, Martin Segura A, Rossi M, Ross T, Tirimanna R, Wang B, Zakieh O, Ben-Arzi H, Flach A, Jackson E, Magers S, Olu abara C, Rogers E, Sugden K, Tan H, Veliah S, Walton U, Asif A, Bharwada Y, Bowley D, Broekhuizen A, Cooper L, Evans N, Girdlestone H, Ling C, Mann H, Mehmood N, Mulvenna CL, Rainer N, Trout I, Gujjuri R, Jeyaraman D, Leong E, Singh D, Smith E, Anderton J, Barabas M, Goyal S, Howard D, Joshi A, Mitchell D, Weatherby T, Badminton R, Bird R, Burtle D, Choi NY, Devalia K, Farr E, Fischer F, Fish J, Gunn F, Jacobs D, Johnston P, Kalakoutas A, Lau E, Loo YNAF, Louden H, Makariou N, Mohammadi K, Nayab Y, Ruhomaun S, Ryliskyte R, Saeed M, Shinde P, Sudul M, Theodoropoulou K, Valadao-Spoorenberg J, Vlachou F, Arshad SR, Janmohamed AM, Noor M, Oyerinde O, Saha A, Syed Y, Watkinson W, Ahmadi H, Akintunde A, Alsaady A, Bradley J, Brothwood D, Burton M, Higgs M, Hoyle C, Katsura C, Lathan R, Louani A, Mandalia R, Prihartadi AS, Qaddoura B, Sandland-Taylor L, Thadani S, Thompson A, Walshaw J, Teo S, Ali S, Bawa JH, Fox S, Gargan K, Haider SA, Hanna N, Hatoum A, Khan Z, Krzak AM, Li T, Pitt J, Tan GJS, Ullah Z, Wilson E, Cleaver J, Colman J, Copeland L, Coulson A, Davis P, Faisal H, Hassan F, Hughes JT, Jabr Y, Mahmoud Ali F, Nahaboo Solim ZN, Sangheli A, Shaya S, Thompson R, Cornwall H, De Andres Crespo M, Fay E, Findlay J, Groves E, Jones O, Killen A, Millo J, Thomas S, Ward J, Wilkins M, Zaki F, Zilber E, Bhavra K, Bilolikar A, Charalambous M, Elawad A, Eleni A, Fawdon R, Gibbins A, Livingstone D, Mala D, Oke SE, Padmakumar D, Patsalides MA, Payne D, Ralphs C, Roney A, Sardar N, Stefanova K, Surti F, Timms R, Tosney G, Bannister J, Clement NS, Cullimore V, Kamal F, Lendor J, McKay J, Mcswiggan J, Minhas N, Seneviratne K, Simeen S, Valverde J, Watson N, Bloom I, Dinh TH, Hirniak J, Joseph R, Kansagra M, Lai CKN, Melamed N, Patel J, Randev J, Sedighi T, Shurovi B, Sodhi J, Vadgama N, Abdulla S, Adabavazeh B, Champion A, Chennupati R, Chu K, Devi S, Haji A, Schulz J, Testa F, Davies P, Gurung B, Howell S, Modi P, Pervaiz A, Zahid M, Abdolrazaghi S, Abi Aoun R, Anjum Z, Bawa G, Bhardwaj R, Brown S, Enver M, Gill D, Gopikrishna D, Gurung D, Kanwal A, Kaushal P, Khanna A, Lovell E, McEvoy C, Mirza M, Nabeel S, Naseem S, Pandya K, Perkins R, Pulakal R, Ray M, Reay C, Reilly S, Round A, Seehra J, Shakeel NM, Singh B, Vijay Sukhnani M, Brown L, Desai B, Elzanati H, Godhaniya J, Kavanagh E, Kent J, Kishor A, Liu A, Norwood M, Shaari N, Wood C, Wood M, Brown A, Chellapuri A, Ferriman A, Ghosh I, Kulkarni N, Noton T, Pinto A, Rajesh S, Varghese B, Wenban C, Aly R, Barciela C, Brookes T, Corrin E, Goldsworthy M, Mohamed Azhar MS, Moore J, Nakhuda S, Ng D, Pillay S, Port S, Abdullah M, Akinyemi J, Islam S, Kale A, Lewis A, Manjunath T, McCabe H, Misra S, Stubley T, Tam JP, Waraich N, Chaora T, Ford C, Osinkolu I, Pong G, Rai J, Risquet R, Ainsworth J, Ayandokun P, Barham E, Barrett G, Barry J, Bisson E, Bridges I, Burke D, Cann J, Cloney M, Coates S, Cripps P, Davies C, Francis N, Green S, Handley G, Hathaway D, Hurt L, Jenkins S, Johnston C, Khadka A, McGee U, Morris D, Murray R, Norbury C, Pierrepont Z, Richards C, Ross O, Ruddy A, Salmon C, Shield M, Soanes K, Spencer N, Taverner S, Williams C, Wills-Wood W, Woodward S, Chow J, Fan J, Guest O, Hunter I, Moon WY, Arthur-Quarm S, Edwards P, Hamlyn V, McEneaney L, N D G, Pranoy S, Ting M, Abada S, Alawattegama LH, Ashok A, Carey C, Gogna A, Haglund C, Hurley P, Leelo N, Liu B, Mannan F, Paramjothy K, Ramlogan K, Raymond-Hayling O, Shanmugarajah A, Solichan D, Wilkinson B, Ahmad NA, Allan D, Amin A, Bakina C, Burns F, Cameron F, Campbell A, Cavanagh S, Chan SMZ, Chapman S, Chong V, Edelsten E, Ekpete O, El Sheikh M, Ghose R, Hassane A, Henderson C, Hilton-Christie S, Husain M, Hussain H, Javid Z, Johnson-Ogbuneke J, Johnston A, Khalil M, Leung TCC, Makin I, Muralidharan V, Naeem M, Patil P, Ravichandran S, Saraeva D, Shankey-Smith W, Sharma N, Swan R, Waudby-West R, Wilkinson A, Wright K, Balasubramanian A, Bhatti S, Chalkley M, Chou WK, Dixon M, Evans L, Fisher K, Gandhi P, Ho S, Lau YB, Lowe S, Meechan C, Murali N, Musonda C, Njoku P, Ochieng L, Pervez MU, Seebah K, Shaikh I, Sikder MA, Vanker R, Alom J, Bajaj V, Coleman O, Finch G, Goss J, Jenkins C, Kontothanassis A, Liew MS, Ng K, Outram M, Shakeel MM, Tawn J, Zuhairy S, Chapple K, Cinnamond A, Coleman S, George HA, Goulder L, Hare N, Hawksley J, Kret A, Luesley A, Mecia L, Porter H, Puddy E, Richardson G, Sohail B, Srikaran V, Tadross D, Tobin J, Tokidis E, Young L, Ashdown T, Bratsos S, Koomson A, Kufuor A, Lim MQ, Shah S, Thorne EPC, Warusavitarne J, Xu S, Abigail S, Ahmed A, Ahmed J, Akmal A, Al-Khafaji M, Amini B, Arshad M, Bogie E, Brazkiewicz M, Carroll M, Chandegra A, Cirelli C, Deng A, Fairclough S, Fung YJ, Gornell C, Green RL, Green SV, Gulamhussein AHM, Isaac AG, Jan R, Jegatheeswaran L, Knee M, Kotecha J, Kotecha S, Maxwell-Armstrong C, McIntyre C, Mendis N, Naing TKP, Oberman J, Ong ZX, Ramalingam A, Saeed Adam A, Tan LL, Towell S, Yadav J, Anandampillai R, Chung S, Hounat A, Ibrahim B, Jeyakumar G, Khalil A, Khan UA, Nair G, Owusu-Ayim M, Wilson M, Kanani A, Kilkelly B, Ogunmwonyi I, Ong L, Samra B, Schomerus L, Shea J, Turner O, Yang Y, Amin M, Blott N, Clark A, Feather A, Forrest M, Hague S, Hamilton K, Higginbotham G, Hope E, Karimian S, Loveday K, Malik H, McKenna O, Noor A, Onsiong C, Patel B, Radcliffe N, Shah P, Tye L, Verma K, Walford R, Yusufi U, Zachariah M, Casey A, Doré C, Fludder V, Fortescue L, Kalapu SS, Karel E, Khera G, Smith C, Appleton B, Ashaye A, Boggon E, Evans A, Faris Mahmood H, Hinchcliffe Z, Marei O, Silva I, Spooner C, Thomas G, Timlin M, Wellington J, Yao SL, Abdelrazek M, Abdelrazik Y, Bee F, Joseph A, Mounce A, Parry G, Vignarajah N, Biddles D, Creissen A, Kolhe S, K T, Lea A, Ledda V, O'Loughlin P, Scanlon J, Shetty N, Weller C, Abdalla M, Adeoye A, Bhatti M, Chadda KR, Chu J, Elhakim H, Foster-Davies H, Rabie M, Tailor B, Webb S, Abdelrahim ASA, Choo SY, Jiwa A, Mangam S, Murray S, Shandramohan A, Aghanenu O, Budd W, Hayre J, Khanom S, Liew ZY, McKinney R, Moody N, Muhammad-Kamal H, Odogwu J, Patel D, Roy C, Sattar Z, Shahrokhi N, Sinha I, Thomson E, Wonga L, Bain J, Khan J, Ricardo D, Bevis R, Cherry C, Darkwa S, Drew W, Griffiths E, Konda N, Madani D, Mak JKC, Meda B, Odunukwe U, Preest G, Raheel F, Rajaseharan A, Ramgopal A, Risbrooke C, Selvaratnam K, Sethunath G, Tabassum R, Taylor J, Thakker A, Wijesingha N, Wybrew R, Yasin T, Ahmed Osman A, Alfadhel S, Carberry E, Chen JY, Drake I, Glen P, Jayasuriya N, Kawar L, Myatt R, Sinan LOH, Siu SSY, Tjen V, Adeboyejo O, Bacon H, Barnes R, Birnie C, D'Cunha Kamath A, Hughes E, Middleton S, Owen R, Schofield E, Short C, Smith R, Wang H, Willett M, Zimmerman M, Balfour J, Chadwick T, Coombe-Jones M, Do Le HP, Faulkner G, Hobson K, Shehata Z, Beattie M, Chmielewski G, Chong C, Donnelly B, Drusch B, Ellis J, Farrelly C, Feyi-Waboso J, Hibell I, Hoade L, Ho C, Jones H, Kodiatt B, Lidder P, Ni Cheallaigh L, Norman R, Patabendi I, Penfold H, Playfair M, Pomeroy S, Ralph C, Rottenburg H, Sebastian J, Sheehan M, Stanley V, Welchman J, Ajdarpasic D, Antypas A, Azouaghe O, Basi S, Bettoli G, Bhattarai S, Bommireddy L, Bourne K, Budding J, Cookey-Bresi R, Cummins T, Davies G, Fabelurin C, Gwilliam R, Hanley J, Hird A, Kruczynska A, Langhorne B, Lund J, Lutchman I, McGuinness R, Neary M, Pampapathi S, Pang E, Podbicanin S, Rai N, Redhouse White G, Sujith J, Thomas P, Walker I, Winterton R, Anderson P, Barrington M, Bhadra K, Clark G, Fowler G, Gibson C, Hudson S, Kaminskaite V, Lawday S, Longshaw A, MacKrill E, McLachlan F, Murdeshwar A, Nieuwoudt R, Parker P, Randall R, Rawlins E, Reeves SA, Rye D, Sirkis T, Sykes B, Ventress N, Wosinska N, Akram B, Burton L, Coombs A, Long R, Magowan D, Ong C, Sethi M, Williams G, Chan C, Chan LH, Fernando D, Gaba F, Khor Z, Les JW, Mak R, Moin S, Ng Kee Kwong KC, Paterson-Brown S, Tew YY, Bardon A, Burrell K, Coldwell C, Costa I, Dexter E, Hardy A, Khojani M, Mazurek J, Raymond T, Reddy V, Reynolds J, Soma A, Agiotakis S, Alsusa H, Desai N, Peristerakis I, Adcock A, Ayub H, Bennett T, Bibi F, Brenac S, Chapman T, Clarke G, Clark F, Galvin C, Gwyn-Jones A, Henry-Blake C, Kerner S, Kiandee M, Lovett A, Pilecka A, Ravindran R, Siddique H, Sikand T, Treadwell K, Akmal K, Apata A, Barton O, Broad G, Darling H, Dhuga Y, Emms L, Habib S, Jain R, Jeater J, Kan CYP, Kathiravelupillai A, Khatkar H, Kirmani S, Kulasabanathan K, Lacey H, Lal K, Manafa C, Mansoor M, McDonald S, Mittal A, Mustoe S, Nottrodt L, Oliver P, Papapetrou I, Pattinson F, Raja M, Reyhani H, Shahmiri A, Small O, Soni U, Aguirrezabala Armbruster B, Bunni J, Hakim MA, Hawkins-Hooker L, Howell KA, Hullait R, Jaskowska A, Ottewell L, Thomas-Jones I, Vasudev A, Clements B, Fenton J, Gill M, Haider S, Lim AJM, Maguire H, McMullan J, Nicoletti J, Samuel S, Unais MA, White N, Yao PC, Yow L, Boyle C, Brady R, Cheekoty P, Cheong J, Chew SJHL, Chow R, Ganewatta Kankanamge D, Mamer L, Mohammed B, Ng Chieng Hin J, Renji Chungath R, Royston A, Sharrad E, Sinclair R, Tingle S, Treherne K, Wyatt F, Maniarasu VS, Moug S, Appanna T, Bucknall T, Hussain F, Owen A, Parry M, Parry R, Sagua N, Spofforth K, Yuen ECT, Bosley N, Hardie W, Moore T, Regas C, Abdel-Khaleq S, Ali N, Bashiti H, Buxton-Hopley R, Constantinides M, D'Afflitto M, Deshpande A, Duque Golding J, Frisira E, Germani Batacchi M, Gomaa A, Hay D, Hutchison R, Iakovou A, Iakovou D, Ismail E, Jefferson S, Jones L, Khouli Y, Knowles C, Mason J, McCaughan R, Moffatt J, Morawala A, Nadir H, Neyroud F, Nikookam Y, Parmar A, Pinto L, Ramamoorthy R, Richards E, Thomson S, Trainer C, Valetopoulou A, Vassiliou A, Wantman A, Wilde S, Dickinson M, Rockall T, Senn D, Wcislo K, Zalmay P, Adelekan K, Allen K, Bajaj M, Gatumbu P, Hang S, Hashmi Y, Kaur T, Kawesha A, Kisiel A, Woodmass M, Adelowo T, Ahari D, Alhwaishel K, Atherton R, Clayton B, Cockroft A, Curtis Lopez C, Hilton M, Ismail N, Kouadria M, Lee L, MacConnachie A, Monks F, Mungroo S, Nikoletopoulou C, Pearce L, Sara X, Shahid A, Suresh G, Wilcha R, Atiyah A, Davies E, Dermanis A, Gibbons H, Hyde A, Lawson A, Lee C, Leung-Tack M, Li Saw Hee J, Mostafa O, Nair D, Pattani N, Plumbley-Jones J, Pufal K, Ramesh P, Sanghera J, Saram S, Scadding S, See S, Stringer H, Torrance A, Vardon H, Wyn-Griffiths F, Brew A, Kaur G, Soni D, Tickle A, Akbar Z, Appleyard T, Figg K, Jayawardena P, Johnson A, Kamran Siddiqui Z, Lacy-Colson J, Oatham R, Rowlands B, Sludden E, Turnbull C, Allin D, Ansar Z, Azeez Z, Dale VH, Garg J, Horner A, Jones S, Knight S, McGregor C, McKenna J, McLelland T, Packham-Smith A, Rowsell K, Spector-Hill I, Adeniken E, Baker J, Bartlett M, Chikomba L, Connell B, Deekonda P, Dhar M, Elmansouri A, Gamage K, Goodhew R, Hanna P, Knight J, Luca A, Maasoumi N, Mahamoud F, Manji S, Marwaha PK, Mason F, Oluboyede A, Pigott L, Razaq AM, Richardson M, Saddaoui I, Wijeyendram P, Yau S, Atkins W, Liang K, Miles N, Praveen B, Ashai S, Braganza J, Common J, Cundy A, Davies R, Guthrie J, Handa I, Iqbal M, Ismail R, Jones C, Jones I, Lee KS, Levene A, Okocha M, Olivier J, Smith A, Subramaniam E, Tandle S, Wang A, Watson A, Wilson C, Chan XHF, Khoo E, Montgomery C, Norris M, Pugalenthi PP, Common T, Cook E, Mistry H, Shinmar HS, Agarwal G, Bandyopadhyay S, Brazier B, Carroll L, Goede A, Harbourne A, Lakhani A, Lami M, Larwood J, Martin J, Merchant J, Pattenden S, Pradhan A, Raafat N, Rothwell E, Shammoon Y, Sudarshan R, Vickers E, Wingfield L, Ashworth I, Azizi S, Bhate R, Chowdhury T, Christou A, Davies L, Dwaraknath M, Farah Y, Garner J, Gureviciute E, Hart E, Jain A, Javid S, Kankam HK, Kaur Toor P, Kaz R, Kermali M, Khan I, Mattson A, McManus A, Murphy M, Nair K, Ngemoh D, Norton E, Olabiran A, Parry L, Payne T, Pillai K, Price S, Punjabi K, Raghunathan A, Ramwell A, Raza M, Ritehnia J, Simpson G, Smith W, Sodeinde S, Studd L, Subramaniam M, Thomas J, Towey S, Tsang E, Tuteja D, Vasani J, Vio M, Badran A, Adams J, Anthony Wilkinson J, Asvandi S, Austin T, Bald A, Bix E, Carrick M, Chander B, Chowdhury S, Cooper Drake B, Crosbie S, D Portela S, Francis D, Gallagher C, Gillespie R, Gravett H, Gupta P, Ilyas C, James G, Johny J, Jones A, Kinder F, MacLeod C, Macrow C, Maqsood-Shah A, Mather J, McCann L, McMahon R, Mitham E, Mohamed M, Munton E, Nightingale K, O'Neill K, Onyemuchara I, Senior R, Shanahan A, Sherlock J, Spyridoulias A, Stavrou C, Stokes D, Tamang R, Taylor E, Trafford C, Uden C, Waddington C, Yassin D, Zaman M, Bangi S, Cheng T, Chew D, Hussain N, Imani-Masouleh S, Mahasivam G, McKnight G, Ng HL, Ota HC, Pasha T, Ravindran W, Shah K, Vishnu K S, Zaman S, Carr W, Cope S, Eagles EJ, Howarth-Maddison M, Li CY, Reed J, Ridge A, Stubbs T, Teasdaled D, Umar R, Worthington J, Dhebri A, Kalenderov R, Alattas A, Arain Z, Bhudia R, Chia D, Daniel S, Dar T, Garland H, Girish M, Hampson A, Kyriacou H, Lehovsky K, Mullins W, Omorphos N, Vasdev N, Venkatesh A, Waldock W, Bhandari A, Brown G, Choa G, Eichenauer CE, Ezennia K, Kidwai Z, Lloyd-Thomas A, Macaskill Stewart A, Massardi C, Sinclair E, Skajaa N, Smith M, Tan I, Afsheen N, Anuar A, Azam Z, Bhatia P, Davies-kelly N, Dickinson S, Elkawafi M, Ganapathy M, Gupta S, Khoury EG, Licudi D, Mehta V, Neequaye S, Nita G, Tay VL, Zhao S, Botsa E, Cuthbert H, Elliott J, Furlepa M, Lehmann J, Mangtani A, Narayan A, Nazarian S, Parmar C, Shah D, Shaw C, Zhao Z, Beck C, Caldwell S, Clements JM, French B, Kenny R, Kirk S, Lindsay J, McClung A, McLaughlin N, Watson S, Whiteside E, Alyacoubi S, Arumugam V, Beg R, Dawas K, Garg S, Lloyd ER, Mahfouz Y, Manobharath N, Moonesinghe R, Morka N, Patel K, Prashar J, Yip S, Adeeko ES, Ajekigbe F, Bhat A, Evans C, Farrugia A, Gurung C, Long T, Malik B, Manirajan S, Newport D, Rayer J, Ridha A, Ross E, Saran T, Sinker A, Waruingi D, Allen R, Al Sadek Y, Alves do Canto Brum H, Asharaf H, Ashman M, Balakumar V, Barrington J, Baskaran R, Berry A, Bhachoo H, Bilal A, Boaden L, Chia WL, Covell G, Crook D, Dadnam F, Davis L, De Berker H, Doyle C, Fox C, Gruffydd-Davies M, Hafouda Y, Hill A, Hubbard E, Hunter A, Inpadhas V, Jamshaid M, Jandu G, Jeyanthi M, Jones T, Kantor C, Kwak SY, Malik N, Matt R, McNulty P, Miles C, Mohomed A, Myat P, Niharika J, Nixon A, O'Reilly D, Parmar K, Pengelly S, Price L, Ramsden M, Turnor R, Wales E, Waring H, Wu M, Yang T, Ye TTS, Zander A, Zeicu C, Bellam S, Francombe J, Kawamoto N, Rahman MR, Sathyanarayana A, Tang HT, Cheung J, Hollingshead J, Page V, Sugarman J, Wong E, Chiong J, Fung E, Kan SY, Kiang J, Kok J, Krahelski O, Liew MY, Lyell B, Sharif Z, Speake D, Alim L, Amakye NY, Chandrasekaran J, Chandratreya N, Drake J, Owoso T, Thu YM, Abou El Ela Bourquin B, Alberts J, Chapman D, Rehnnuma N, Ainsworth K, Carpenter H, Emmanuel T, Fisher T, Gabrel M, Guan Z, Hollows S, Hotouras A, Ip Fung Chun N, Jaffer S, Kallikas G, Kennedy N, Lewinsohn B, Liu FY, Mohammed S, Rutherfurd A, Situ T, Stammer A, Taylor F, Thin N, Urgesi E, Zhang N, Ahmad MA, Bishop A, Bowes A, Dixit A, Glasson R, Hatta S, Hatt K, Larcombe S, Preece J, Riordan E, Fegredo D, Haq MZ, Li C, McCann G, Stewart D, Baraza W, Bhullar D, Burt G, Coyle J, Deans J, Devine A, Hird R, Ikotun O, Manchip G, Ross C, Storey L, Tan WWL, Tse C, Warner C, Whitehead M, Wu F, Court EL, Crisp E, Huttman M, Mayes F, Robertson H, Rosen H, Sandberg C, Smith H, Al Bakry M, Ashwell W, Bajaj S, Bandyopadhyay D, Browlee O, Burway S, Chand CP, Elsayeh K, Elsharkawi A, Evans E, Ferrin S, Fort-Schaale A, Iacob M, I K, Impelliziere Licastro G, Mankoo AS, Olaniyan T, Otun J, Pereira R, Reddy R, Saeed D, Simmonds O, Singhal G, Tron K, Wickstone C, Williams R, Bradshaw E, De Kock Jewell V, Houlden C, Knight C, Metezai H, Mirza-Davies A, Seymour Z, Spink D, Wischhusen S. Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study. Lancet Digit Health 2022; 4:e520-e531. [PMID: 35750401 DOI: 10.1016/s2589-7500(22)00069-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/07/2022] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications. METHODS We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC). FINDINGS In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683-0·717]). INTERPRETATION In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required. FUNDING British Journal of Surgery Society.
Collapse
|
3
|
Gupta P, Naithani S, Preece J, Kim S, Cheng T, D'Eustachio P, Elser J, Bolton EE, Jaiswal P. Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. Methods Mol Biol 2022; 2443:511-525. [PMID: 35037224 DOI: 10.1007/978-1-0716-2067-0_27] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plant Reactome (https://plantreactome.gramene.org) and PubChem ( https://pubchem.ncbi.nlm.nih.gov ) are two reference data portals and resources for curated plant pathways, small molecules, metabolites, gene products, and macromolecular interactions. Plant Reactome knowledgebase, a conceptual plant pathway network, is built by biocuration and integrating (bio)chemical entities, gene products, and macromolecular interactions. It provides manually curated pathways for the reference species Oryza sativa (rice) and gene orthology-based projections that extend pathway knowledge to 106 plant species. Currently, it hosts 320 reference pathways for plant metabolism, hormone signaling, transport, genetic regulation, plant organ development and differentiation, and biotic and abiotic stress responses. In addition to the pathway browsing and search functions, the Plant Reactome provides the analysis tools for pathway comparison between reference and projected species, pathway enrichment in gene expression data, and overlay of gene-gene interaction data on pathways. PubChem, a popular reference database of (bio)chemical entities, provides information on small molecules and other types of chemical entities, such as siRNAs, miRNAs, lipids, carbohydrates, and chemically modified nucleotides. The data in PubChem is collected from hundreds of data sources, including Plant Reactome. This chapter provides a brief overview of the Plant Reactome and the PubChem knowledgebases, their association to other public resources providing accessory information, and how users can readily access the contents.
Collapse
Affiliation(s)
- Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Sunghwan Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Tiejun Cheng
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Evan E Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
| |
Collapse
|
4
|
Yates AD, Allen J, Amode RM, Azov AG, Barba M, Becerra A, Bhai J, Campbell LI, Carbajo Martinez M, Chakiachvili M, Chougule K, Christensen M, Contreras-Moreira B, Cuzick A, Da Rin Fioretto L, Davis P, De Silva NH, Diamantakis S, Dyer S, Elser J, Filippi CV, Gall A, Grigoriadis D, Guijarro-Clarke C, Gupta P, Hammond-Kosack KE, Howe KL, Jaiswal P, Kaikala V, Kumar V, Kumari S, Langridge N, Le T, Luypaert M, Maslen GL, Maurel T, Moore B, Muffato M, Mushtaq A, Naamati G, Naithani S, Olson A, Parker A, Paulini M, Pedro H, Perry E, Preece J, Quinton-Tulloch M, Rodgers F, Rosello M, Ruffier M, Seager J, Sitnik V, Szpak M, Tate J, Tello-Ruiz MK, Trevanion SJ, Urban M, Ware D, Wei S, Williams G, Winterbottom A, Zarowiecki M, Finn RD, Flicek P. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Res 2021; 50:D996-D1003. [PMID: 34791415 PMCID: PMC8728113 DOI: 10.1093/nar/gkab1007] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 11/28/2022] Open
Abstract
Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here, we present our largest increase in plant, metazoan and fungal genomes since the project's inception creating one of the world's most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We detail our new efforts in gene annotation, our emerging support for pangenome analysis, our efforts to accelerate data dissemination through the Ensembl Rapid Release resource and our new AlphaFold visualization. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl's release cycle.
Collapse
Affiliation(s)
- Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ridwan M Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrey G Azov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Barba
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrés Becerra
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jyothish Bhai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lahcen I Campbell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Manuel Carbajo Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Chakiachvili
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Mikkel Christensen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alayne Cuzick
- Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Luca Da Rin Fioretto
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nishadi H De Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stavros Diamantakis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Carla V Filippi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dionysios Grigoriadis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cristina Guijarro-Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Kim E Hammond-Kosack
- Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Vinay Kaikala
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vivek Kumar
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Nick Langridge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tuan Le
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Manuel Luypaert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gareth L Maslen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aleena Mushtaq
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Paulini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helder Pedro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Mark Quinton-Tulloch
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Faye Rodgers
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Marc Rosello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Seager
- Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Vasily Sitnik
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michal Szpak
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - John Tate
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Martin Urban
- Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Doreen Ware
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.,USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Gary Williams
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrea Winterbottom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magdalena Zarowiecki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| |
Collapse
|
5
|
Warman C, Sullivan CM, Preece J, Buchanan ME, Vejlupkova Z, Jaiswal P, Fowler JE. A cost-effective maize ear phenotyping platform enables rapid categorization and quantification of kernels. Plant J 2021; 106:566-579. [PMID: 33476427 DOI: 10.1111/tpj.15166] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/30/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
High-throughput phenotyping systems are powerful, dramatically changing our ability to document, measure, and detect biological phenomena. Here, we describe a cost-effective combination of a custom-built imaging platform and deep-learning-based computer vision pipeline. A minimal version of the maize (Zea mays) ear scanner was built with low-cost and readily available parts. The scanner rotates a maize ear while a digital camera captures a video of the surface of the ear, which is then digitally flattened into a two-dimensional projection. Segregating GFP and anthocyanin kernel phenotypes are clearly distinguishable in ear projections and can be manually annotated and analyzed using image analysis software. Increased throughput was attained by designing and implementing an automated kernel counting system using transfer learning and a deep learning object detection model. The computer vision model was able to rapidly assess over 390 000 kernels, identifying male-specific transmission defects across a wide range of GFP-marked mutant alleles. This includes a previously undescribed defect putatively associated with mutation of Zm00001d002824, a gene predicted to encode a vacuolar processing enzyme. Thus, by using this system, the quantification of transmission data and other ear and kernel phenotypes can be accelerated and scaled to generate large datasets for robust analyses.
Collapse
Affiliation(s)
- Cedar Warman
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Christopher M Sullivan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Justin Preece
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Michaela E Buchanan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Zuzana Vejlupkova
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Pankaj Jaiswal
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - John E Fowler
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| |
Collapse
|
6
|
Warman C, Sullivan CM, Preece J, Buchanan ME, Vejlupkova Z, Jaiswal P, Fowler JE. A cost-effective maize ear phenotyping platform enables rapid categorization and quantification of kernels. Plant J 2021; 106:566-579. [PMID: 33476427 DOI: 10.1101/2020.07.12.199000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/30/2020] [Accepted: 01/13/2021] [Indexed: 05/24/2023]
Abstract
High-throughput phenotyping systems are powerful, dramatically changing our ability to document, measure, and detect biological phenomena. Here, we describe a cost-effective combination of a custom-built imaging platform and deep-learning-based computer vision pipeline. A minimal version of the maize (Zea mays) ear scanner was built with low-cost and readily available parts. The scanner rotates a maize ear while a digital camera captures a video of the surface of the ear, which is then digitally flattened into a two-dimensional projection. Segregating GFP and anthocyanin kernel phenotypes are clearly distinguishable in ear projections and can be manually annotated and analyzed using image analysis software. Increased throughput was attained by designing and implementing an automated kernel counting system using transfer learning and a deep learning object detection model. The computer vision model was able to rapidly assess over 390 000 kernels, identifying male-specific transmission defects across a wide range of GFP-marked mutant alleles. This includes a previously undescribed defect putatively associated with mutation of Zm00001d002824, a gene predicted to encode a vacuolar processing enzyme. Thus, by using this system, the quantification of transmission data and other ear and kernel phenotypes can be accelerated and scaled to generate large datasets for robust analyses.
Collapse
Affiliation(s)
- Cedar Warman
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Christopher M Sullivan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Justin Preece
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Michaela E Buchanan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Zuzana Vejlupkova
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Pankaj Jaiswal
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - John E Fowler
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| |
Collapse
|
7
|
Tello-Ruiz MK, Naithani S, Gupta P, Olson A, Wei S, Preece J, Jiao Y, Wang B, Chougule K, Garg P, Elser J, Kumari S, Kumar V, Contreras-Moreira B, Naamati G, George N, Cook J, Bolser D, D'Eustachio P, Stein LD, Gupta A, Xu W, Regala J, Papatheodorou I, Kersey PJ, Flicek P, Taylor C, Jaiswal P, Ware D. Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res 2021; 49:D1452-D1463. [PMID: 33170273 DOI: 10.1093/nar/gkaa979] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/09/2020] [Indexed: 01/27/2023] Open
Abstract
Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes-over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene-gene interactions. Gramene integrates ontology-based protein structure-function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome.
Collapse
Affiliation(s)
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Yinping Jiao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Priyanka Garg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Vivek Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Nancy George
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Justin Cook
- Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto M5G 1L7, Canada
| | - Daniel Bolser
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK.,Current affiliation: Geromics Inc., Cambridge CB1 3NF, UK
| | - Peter D'Eustachio
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Lincoln D Stein
- Adaptive Oncology Program, Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Amit Gupta
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX 78758, USA
| | - Weijia Xu
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX 78758, USA
| | - Jennifer Regala
- American Society of Plant Biologists, Rockville, MD 20855-2768, USA.,Current affiliation: American Urological Association, Linthicum, MD 21090, USA
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Paul J Kersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK.,Current affiliation: Royal Botanic Gardens, Kew Richmond, Surrey TW9 3AE, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Crispin Taylor
- American Society of Plant Biologists, Rockville, MD 20855-2768, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| |
Collapse
|
8
|
Tello-Ruiz MK, Naithani S, Gupta P, Olson A, Wei S, Preece J, Jiao Y, Wang B, Chougule K, Garg P, Elser J, Kumari S, Kumar V, Contreras-Moreira B, Naamati G, George N, Cook J, Bolser D, D'Eustachio P, Stein LD, Gupta A, Xu W, Regala J, Papatheodorou I, Kersey PJ, Flicek P, Taylor C, Jaiswal P, Ware D. Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res 2021; 49:D1452-D1463. [PMID: 33170273 DOI: 10.1093/nar/gkaa979/5973447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/09/2020] [Indexed: 05/20/2023] Open
Abstract
Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes-over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene-gene interactions. Gramene integrates ontology-based protein structure-function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome.
Collapse
Affiliation(s)
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Yinping Jiao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Priyanka Garg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Vivek Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Nancy George
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Justin Cook
- Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto M5G 1L7, Canada
| | - Daniel Bolser
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
- Current affiliation: Geromics Inc., Cambridge CB1 3NF, UK
| | - Peter D'Eustachio
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Lincoln D Stein
- Adaptive Oncology Program, Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Amit Gupta
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX 78758, USA
| | - Weijia Xu
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX 78758, USA
| | - Jennifer Regala
- American Society of Plant Biologists, Rockville, MD 20855-2768, USA
- Current affiliation: American Urological Association, Linthicum, MD 21090, USA
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Paul J Kersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
- Current affiliation: Royal Botanic Gardens, Kew Richmond, Surrey TW9 3AE, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Crispin Taylor
- American Society of Plant Biologists, Rockville, MD 20855-2768, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| |
Collapse
|
9
|
Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W, Allen J, Alvarez-Jarreta J, Barba M, Bolser DM, Cambell L, Carbajo M, Chakiachvili M, Christensen M, Cummins C, Cuzick A, Davis P, Fexova S, Gall A, George N, Gil L, Gupta P, Hammond-Kosack KE, Haskell E, Hunt SE, Jaiswal P, Janacek SH, Kersey PJ, Langridge N, Maheswari U, Maurel T, McDowall MD, Moore B, Muffato M, Naamati G, Naithani S, Olson A, Papatheodorou I, Patricio M, Paulini M, Pedro H, Perry E, Preece J, Rosello M, Russell M, Sitnik V, Staines DM, Stein J, Tello-Ruiz MK, Trevanion SJ, Urban M, Wei S, Ware D, Williams G, Yates AD, Flicek P. Ensembl Genomes 2020-enabling non-vertebrate genomic research. Nucleic Acids Res 2020; 48:D689-D695. [PMID: 31598706 PMCID: PMC6943047 DOI: 10.1093/nar/gkz890] [Citation(s) in RCA: 283] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 09/29/2019] [Accepted: 10/02/2019] [Indexed: 12/28/2022] Open
Abstract
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.
Collapse
Affiliation(s)
- Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nishadi De Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gareth Maslen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Wasiu Akanni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jorge Alvarez-Jarreta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Barba
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dan M Bolser
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lahcen Cambell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Manuel Carbajo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Chakiachvili
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mikkel Christensen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alayne Cuzick
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Paul Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Silvie Fexova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nancy George
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Kim E Hammond-Kosack
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Erin Haskell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sophie H Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul J Kersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nick Langridge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Uma Maheswari
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mark D McDowall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ben Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Paulini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helder Pedro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marc Rosello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Russell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vasily Sitnik
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel M Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joshua Stein
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | | | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Martin Urban
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Sharon Wei
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.,USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
| | - Gary Williams
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| |
Collapse
|
10
|
Naithani S, Gupta P, Preece J, D'Eustachio P, Elser JL, Garg P, Dikeman DA, Kiff J, Cook J, Olson A, Wei S, Tello-Ruiz MK, Mundo AF, Munoz-Pomer A, Mohammed S, Cheng T, Bolton E, Papatheodorou I, Stein L, Ware D, Jaiswal P. Plant Reactome: a knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res 2020; 48:D1093-D1103. [PMID: 31680153 PMCID: PMC7145600 DOI: 10.1093/nar/gkz996] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 12/29/2022] Open
Abstract
Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model and framework. It currently hosts 298 reference pathways, including metabolic and transport pathways, transcriptional networks, hormone signaling pathways, and plant developmental processes. In addition to browsing plant pathways, users can upload and analyze their omics data, such as the gene-expression data, and overlay curated or experimental gene-gene interaction data to extend pathway knowledge. The curation team actively engages researchers and students on gene and pathway curation by offering workshops and online tutorials. The Plant Reactome supports, implements and collaborates with the wider community to make data and tools related to genes, genomes, and pathways Findable, Accessible, Interoperable and Re-usable (FAIR).
Collapse
Affiliation(s)
- Sushma Naithani
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Parul Gupta
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Justin Preece
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
| | | | - Justin L Elser
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Priyanka Garg
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Daemon A Dikeman
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Jason Kiff
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Justin Cook
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | - Alfonso Munoz-Pomer
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | - Suhaib Mohammed
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | - Tiejun Cheng
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Evan Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Irene Papatheodorou
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | - Lincoln Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,USDA-ARS, RW Holley Center for Agriculture & Health, Ithaca, NY, USA
| | - Pankaj Jaiswal
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
| |
Collapse
|
11
|
Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D'Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D. Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res 2019; 46:D1181-D1189. [PMID: 29165610 PMCID: PMC5753211 DOI: 10.1093/nar/gkx1111] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/25/2017] [Indexed: 12/24/2022] Open
Abstract
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations. Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks. Specifically, it uses curated rice reference pathways to derive pathway projections for an additional 66 species based on gene orthology, and facilitates display of gene expression, gene-gene interactions, and user-defined omics data in the context of these pathways. As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes periodic data and software upgrades. Via powerful, intuitive search interfaces, users can easily query across various portals and interactively analyze search results by clicking on diverse features such as genomic context, highly augmented gene trees, gene expression anatomograms, associated pathways, and external informatics resources. All data in Gramene are accessible through both visual and programmatic interfaces.
Collapse
Affiliation(s)
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Joshua C Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Michael Campbell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Matthew J Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Yinping Jiao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Young Koung Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Division of Biological Sciences and Institute for Basic Science, Wonkwang University, Iksan 54538, Korea
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joseph Mulvaney
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Noor Al-Bader
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - James Thomason
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Vivek Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Daniel M Bolser
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Guy Naamati
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Electra Tapanari
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Nuno Fonseca
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Laura Huerta
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Haider Iqbal
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Maria Keays
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | | | - Amy Tang
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Antonio Fabregat
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Peter D'Eustachio
- Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Joel Weiser
- Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto, M5G 1L7, Canada
| | - Lincoln D Stein
- Adaptive Oncology Program, Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada
| | - Robert Petryszak
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Irene Papatheodorou
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Paul J Kersey
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Patti Lockhart
- American Society of Plant Biologists, 15501 Monona Drive, Rockville, MD 20855-2768, USA
| | - Crispin Taylor
- American Society of Plant Biologists, 15501 Monona Drive, Rockville, MD 20855-2768, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
| |
Collapse
|
12
|
Cooper L, Meier A, Laporte MA, Elser JL, Mungall C, Sinn BT, Cavaliere D, Carbon S, Dunn NA, Smith B, Qu B, Preece J, Zhang E, Todorovic S, Gkoutos G, Doonan JH, Stevenson DW, Arnaud E, Jaiswal P. The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. Nucleic Acids Res 2019; 46:D1168-D1180. [PMID: 29186578 PMCID: PMC5753347 DOI: 10.1093/nar/gkx1152] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/21/2017] [Indexed: 01/08/2023] Open
Abstract
The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. The Planteome project is developing a plant gene annotation platform; Planteome Noctua, to facilitate community engagement. All the Planteome ontologies are publicly available and are maintained at the Planteome GitHub site (https://github.com/Planteome) for sharing, tracking revisions and new requests. The annotated data are freely accessible from the ontology browser (http://browser.planteome.org/amigo) and our data repository.
Collapse
Affiliation(s)
- Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Austin Meier
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | | | - Justin L Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Chris Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | - Seth Carbon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nathan A Dunn
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Barry Smith
- Department of Philosophy, University at Buffalo, Buffalo, NY 14260, USA
| | - Botong Qu
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Eugene Zhang
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Sinisa Todorovic
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Georgios Gkoutos
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - John H Doonan
- National Plant Phenomics Centre, Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK
| | | | - Elizabeth Arnaud
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| |
Collapse
|
13
|
Sykes L, Taleb H, Preece J, Williams D, Neef D, Oldham H, Dixon G. WS01-5 A novel class of quorum sensing inhibitors prevent biofilm formation and reduce virulence of respiratory pathogens and are progressing to preclinical development. J Cyst Fibros 2019. [DOI: 10.1016/s1569-1993(19)30121-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
14
|
Sykes L, Taleb H, Rice P, Preece J, Williams D, Neef D, Dixon G. P104 A novel class of compounds that inhibit biofilm formation and reduce the virulence and motility of respiratory pathogens. J Cyst Fibros 2019. [DOI: 10.1016/s1569-1993(19)30398-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
15
|
Naithani S, Gupta P, Preece J, Garg P, Fraser V, Padgitt-Cobb LK, Martin M, Vining K, Jaiswal P. Involving community in genes and pathway curation. Database (Oxford) 2019; 2019:5289625. [PMID: 30649295 PMCID: PMC6334007 DOI: 10.1093/database/bay146] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/11/2018] [Indexed: 12/25/2022]
Abstract
Biocuration plays a crucial role in building databases and complex systems-level platforms required for processing, annotating and analyzing ‘Big Data’ in biology. However, biocuration efforts cannot keep pace with a dramatic increase in the production of omics data; this presents one of the bottlenecks in genomics. In two pathway curation jamborees, Plant Reactome curators tested strategies for introducing researchers to pathway curation tools, harnessing biologists’ expertise in curating plant pathways and developing a network of community biocurators. We summarize the strategy, workflow and outcomes of these exercises, and discuss the role of community biocuration in advancing databases and genomic resources.
Collapse
Affiliation(s)
- Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Priyanka Garg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Valerie Fraser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.,Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, USA
| | | | - Matthew Martin
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Kelly Vining
- Department of Horticulture, Oregon State University, Corvallis, OR, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| |
Collapse
|
16
|
Papatheodorou I, Fonseca NA, Keays M, Tang Y, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AMP, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R. Expression Atlas: gene and protein expression across multiple studies and organisms. Nucleic Acids Res 2018; 46:D246-D251. [PMID: 29165655 PMCID: PMC5753389 DOI: 10.1093/nar/gkx1158] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/26/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022] Open
Abstract
Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, developmental stage, disease or cell type. The available public and controlled access data sets from different sources are curated and re-analysed using standardized, open source pipelines and made available for queries, download and visualization. As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants. Data from large-scale RNA sequencing studies including Blueprint, PCAWG, ENCODE, GTEx and HipSci can be visualized next to each other. In Expression Atlas, users can query genes or gene-sets of interest and explore their expression across or within species, tissues, developmental stages in a constitutive or differential context, representing the effects of diseases, conditions or experimental interventions. All processed data matrices are available for direct download in tab-delimited format or as R-data. In addition to the web interface, data sets can now be searched and downloaded through the Expression Atlas R package. Novel features and visualizations include the on-the-fly analysis of gene set overlaps and the option to view gene co-expression in experiments investigating constitutive gene expression across tissues or other conditions.
Collapse
Affiliation(s)
- Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Nuno A Fonseca
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Maria Keays
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Y Amy Tang
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Elisabet Barrera
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Wojciech Bazant
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Melissa Burke
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | | | - Nancy George
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Laura Huerta
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Satu Koskinen
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Suhaib Mohammed
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | | | | | | | - Andrew F Jarnuczak
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Wolfgang Huber
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Juan Antonio Vizcaino
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Robert Petryszak
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| |
Collapse
|
17
|
Abstract
BACKGROUND Splenogonadal fusion is rare abnormal congenital connection of splenic tissue and gonad. It commonly presents with either cryptorchidism or as a palpable mass. As a benign anomaly, orchiectomy is often unnecessary. Removal of the splenic component may be accomplished with preservation of the testicle. METHODS An 18-month-old boy presented with right cryptorchidism and left retractile testicle. Laparoscopic examination found a viable right testicle, and a successful orchiopexy was performed. The left testicle demonstrated splenogonadal fusion. Discontinuous accessory splenules were noted along the path of testicular descent. After confirmation from a radionucleotide liver-spleen scan the patient was brought back to the operating room for open excision of the adherent splenic tissue and orchiopexy of the testicle via an open inguinal approach. CONCLUSION Splenogonadal fusion is a rare condition, but may be suspected in children with cryptorchidism or palpable peri-testicular mass. As with the present patient, in most cases the splenic tissue may be successfully excised without injury to the testicle.
Collapse
Affiliation(s)
- J Preece
- Department of Pediatric Urology, Nationwide Children's Hospital, Columbus, OH, USA.
| | - S Phillips
- Department of Urology, Charleston Area Medical Center, Charleston, WV, USA
| | - V Sorokin
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - D Herz
- Department of Pediatric Urology, Nationwide Children's Hospital, Columbus, OH, USA
| |
Collapse
|
18
|
Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D’Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P. Gramene Database: Navigating Plant Comparative Genomics Resources. Curr Plant Biol 2016; 7-8:10-15. [PMID: 28713666 PMCID: PMC5509230 DOI: 10.1016/j.cpb.2016.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the annotation of genomic data and provides tools to perform powerful comparative analyses across a wide spectrum of plant species. It consists of an integrated portal for querying, visualizing and analyzing data for 44 plant reference genomes, genetic variation data sets for 12 species, expression data for 16 species, curated rice pathways and orthology-based pathway projections for 66 plant species including various crops. Here we briefly describe the functions and uses of the Gramene database.
Collapse
Affiliation(s)
- Parul Gupta
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Sushma Naithani
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
| | | | | | | | - Antonio Fabregat
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | - Yinping Jiao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Maria Keays
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | | | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Justin Preece
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Joshua Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Joel Weiser
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Laura Huerta
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | - Robert Petryszak
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | - Paul Kersey
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | | | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- USDA ARS NEA Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, NY, USA
| | - Pankaj Jaiswal
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA
- To whom correspondence should be addressed Address of the corresponding author: Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USA, Phone: +1-541-737-8471, Fax: +1-541-737-3573,
| |
Collapse
|
19
|
Naithani S, Preece J, D'Eustachio P, Gupta P, Amarasinghe V, Dharmawardhana PD, Wu G, Fabregat A, Elser JL, Weiser J, Keays M, Fuentes AMP, Petryszak R, Stein LD, Ware D, Jaiswal P. Plant Reactome: a resource for plant pathways and comparative analysis. Nucleic Acids Res 2016; 45:D1029-D1039. [PMID: 27799469 PMCID: PMC5210633 DOI: 10.1093/nar/gkw932] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/27/2016] [Indexed: 12/18/2022] Open
Abstract
Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX.
Collapse
Affiliation(s)
- Sushma Naithani
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Justin Preece
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Peter D'Eustachio
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Parul Gupta
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Vindhya Amarasinghe
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Palitha D Dharmawardhana
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Guanming Wu
- Ontario Institute of Cancer Research, Toronto, ON M5G 0A3, Canada.,Oregon Health & Science University, Portland, OR 97239, USA
| | - Antonio Fabregat
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Justin L Elser
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Joel Weiser
- Ontario Institute of Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Maria Keays
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | | | - Robert Petryszak
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Lincoln D Stein
- Ontario Institute of Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,United States Department of Agriculture - Agriculture Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Pankaj Jaiswal
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| |
Collapse
|
20
|
Velasquez T, Mackey G, Lusk J, Kyle UG, Fontenot T, Marshall P, Shekerdemian LS, Coss-Bu JA, Nishigaki A, Yatabe T, Tamura T, Yamashita K, Yokoyama M, Ruiz-Rodriguez JC, Encina B, Belmonte R, Troncoso I, Tormos P, Riveiro M, Baena J, Sanchez A, Bañeras J, Cordón J, Duran N, Ruiz A, Caballero J, Nuvials X, Riera J, Serra J, Rutten AMF, van Ieperen SNM, Der Kinderen EPHM, Van Logten T, Kovacikova L, Skrak P, Zahorec M, Kyle UG, Akcan-Arikan A, Silva JC, Mackey G, Lusk J, Goldsworthy M, Shekerdemian LS, Coss-Bu JA, Wood D, Harrison D, Parslow R, Davis P, Pappachan J, Goodwin S, Ramnarayan P, Chernyshuk S, Yemets H, Zhovnir V, Pulitano’ SM, De Rosa S, Mancino A, Villa G, Tosi F, Franchi P, Conti G, Patel B, Khine H, Shah A, Sung D, Singer L, Haghbin S, Inaloo S, Serati Z, Idei M, Nomura T, Yamamoto N, Sakai Y, Yoshida T, Matsuda Y, Yamaguchi Y, Takaki S, Yamaguchi O, Goto T, Longani N, Medar S, Abdel-Aal IR, El Adawy AS, Mohammed HMEH, Mohamed AN, Parry SM, Knight LD, Denehy L, De Morton N, Baldwin CE, Sani D, Kayambu G, da Silva VZM, Phongpagdi P, Puthucheary ZA, Granger CL, Rydingsward JE, Horkan CM, Christopher KB, Muscedere J, Scott SH, Saha T, Hamilton A, Petsikas D, Payne D, Boyd JG, Puthucheary ZA, McNelly AS, Rawal J, McWilliams D, Connolly B, McPhail MJ, Sidhu P, Rowlerson A, Moxham J, Harridge SD, Hart N, Montgomery HE, Jovaisa T, Thomas B, Jones C, Gupta D, Wijayatilake DS, Shum HP, King HS, Chan KC, Tang KB, Yan WW, Arias CC, Latorre J, De La Rica AS, Reeves E, Garrido EM, Feijoo AM, Gancedo CH, Tofiño AL, Rodríguez FG, Gemmell LK, Campbell R, Doherty P, MacKay A, Singh N, Atkins G, Vitaller S, Nagib H, Prieto J, Del Arco A, Zayas B, Gomez C, Tirumala S, Pasha SA, Kumari BK, Martinez-Lopez P, Snelson C, Puerto-Morlán A, Nuevo-Ortega P, Pujol LM, Dolset RA, González BS, Riera SQ, Álvarez JT, Quintana S, Martínez L, Algarte R, Aitken LM, Sánchez B, Trenado J, Tomas E, Brock N, Viegas E, Filipe E, Cottle D, Traynor T, Martínez MVT, Márquez MP, Rattray J, Gómez LC, Martínez NA, Muñoz JMM, Bellver BQ, Varea MM, Llorente MÁA, Calvo CP, Hillier SD, Faulds MC, Hendra H, Kenardy J, Lawrence N, Maekawa K, Hayakawa M, Ono Y, Kodate A, Sadamoto Y, Tominaga N, Mizugaki A, Murakami H, Yoshida T, Hull AM, Katabami K, Wada T, Sawamura A, Gando S, Silva S, Kerhuel L, Malagurski B, Citerio G, Chabanne R, Laureys S, Ullman A, Puybasset L, Nobile L, Pognuz ER, Rossetti AO, Verginella F, Gaspard N, Creteur J, Ben-Hamouda N, Oddo M, Taccone FS, Le Brocque R, Ono Y, Hayakawa M, Iijima H, Maekawa K, Kodate A, Sadamoto Y, Mizugaki A, Murakami H, Katabami K, Wada T, Mitchell M, Sawamura A, Gando S, Kodate A, Katabami K, Wada T, Ono Y, Maekawa K, Hayakawa M, Sawamura A, Gando S, Davis C, Andersen LW, Raymond T, Berg R, Nadkarni V, Grossestreuer A, Kurth T, Donnino M, Krüger A, Ostadal P, Janotka M, Macfarlane B, Vondrakova D, Kongpolprom N, Cholkraisuwat J, Pekkarinen PT, Ristagno G, Masson S, Latini R, Bendel S, Ala-Kokko T, Varpula T, Azevedo JC, Vaahersalo J, Hoppu S, Tiainen M, Mion MM, Plebani M, Pettilä V, Skrifvars M, Son Y, Kim KS, Suh GJ, Rocha LL, Kwon WY, Ko JI, Park MJ, Cavicchi FZ, Iesu E, Nobile L, Vincent JL, Creteur J, Taccone FS, Tanaka H, De Freitas FFM, Otani N, Ode S, Ishimatsu S, Martínez L, Algarte R, Sánchez B, Romero I, Martínez F, Quintana S, Trenado J, Cavalheiro AM, Vondrakova D, Ostadal P, Kruger A, Janotka M, Malek F, Neuzil P, Yeh YC, Chen YS, Wang CH, Huang CH, Lucinio NM, Chao A, Lee CT, Lai CH, Chan WS, Cheng YJ, Sun WZ, Kaese S, Horstmann C, Lebiedz P, Mourad M, Lobato MS, Gaudard P, Eliet J, Zeroual N, Colson P, Ostadal P, Mlcek M, Hrachovina M, Kruger A, Vondrakova D, Janotka M, Ebeling G, Mates M, Hala P, Kittnar O, Neuzil P, Jacky A, Rudiger A, Spahn DR, Bettex DA, Kara A, Akin S, Kraegpoeth A, Dos reis Miranda D, Struijs A, Caliskan K, van Thiel RJ, Dubois EA, de Wilde W, Zijlstra F, Gommers D, Ince C, Marca L, Laerkner E, Xini A, Mongkolpun W, Cordeiro CPR, Leite RT, Lheureux O, Bader A, Rincon L, Santacruz C, Preiser JC, Chao A, De Brito-Ashurst I, Chao AS, Chen YS, Kim W, Ahn C, Cho Y, Lim TH, Oh J, Choi KS, Jang BH, Ha JK, White C, Mecklenburg A, Stamm J, Soeffker G, Kubik M, Sydow K, Reichenspurner H, Kluge S, Braune S, Bergantino B, Ruberto F, Gregory S, Magnanimi E, Privato E, Zullino V, Bruno K, Pugliese F, Sales G, Girotto V, Vittone F, Brazzi L, Fritz C, Forni LG, Kimmoun A, Vanhuyse F, Trifan B, Orlowski S, Albuisson E, Tran N, Levy B, Chhor V, Joachim J, Follin A, Flowers E, Champigneulle B, Chatelon J, Fave G, Mantz J, Pirracchio R, Diaz DD, Villanova M, Aguirregabyria M, Andrade G, López L, Curtis A, Palencia E, John G, Cowan R, Hart R, Lake K, Litchfield K, Song JW, Lee YJ, Cho YJ, Choi S, Wood CA, Vermeir P, Vandijck D, Blot S, Mariman A, Verhaeghe R, Deveugele M, Vogelaers D, Chok L, Bachli EB, Bettex D, Siu K, Cottini SR, Keller E, Maggiorini M, Schuepbach R, Fiks T, Stiphout C, Grevelink M, Vaneker I, Ruijter A, Buise M, Venkatesan K, Spronk PE, Tena SA, Barrachina LG, Portillo JHR, Aznar GP, Campos LM, Sellés MDF, Tomás MA, Muncharaz AB, Skinner L, Muhammad JBH, Monsalvo S, Olavarria E, Stümpfle R, Na SJ, Park J, Chung CR, Park CM, Suh GY, Yang JH, Witter T, Ng L, Brousseau C, Butler MB, Erdogan M, Dougall PCM, Green RS, Abbott TEF, Torrance HDT, Cron N, Vaid N, Emmanuel J, Seet E, Siddiqui SS, Prabu N, Chaudhari HK, Patil VP, Divatia JV, Solanki S, Kulkarni AP, Gutierrez LAR, Bader A, Brasseur A, Baptista N, Lheureux O, Vincent JL, Creteur J, Taccone FS, Hempel D, Stauffert N, Recker F, Schröder T, Reusch S, Schleifer J, Escoval A, Breitkreutz R, Sjövall F, Perner A, Møller MH, Moraes RB, Borges FK, Guillen JAV, Zabaletta WJC, Ruiz-Ramos J, Ramirez P, Tomas E, Marqués-Miñana MR, Villarreal E, Gordon M, Sosa M, Concha P, Castellanos A, Menendez R, Ramírez CS, Santana MC, Balcázar LC, Agrawal R, Escalada SH, Viera MAH, Vázquez CFL, Díaz JJD, Campelo FA, Monroy NS, Santana PS, Santana SR, Gutiérrez-Pizarraya A, Garnacho-Montero J, Mathew R, Martin C, Baumstarck K, Leone M, Martín-Loeches I, Pirracchio R, Legrand M, Mainardi JL, Mantz J, Cholley B, Hubbard A, Varma A, Frontera PR, Vega LMC, Miguelena PRDG, Usón MCV, López AR, Clemente EA, Ibañes PG, Aguilar ALR, Palomar M, Olaechea P, Dima E, Uriona S, Vallverdu M, Catalan M, Nuvials X, Aragon C, Lerma FA, Jeon YD, Jeong WY, Kim MH, Jeong IY, Charitidou E, Ahn MY, Ahn JY, Han SH, Choi JY, Song YG, Kim JM, Ku NS, Bassi GL, Xiol EA, Senussi T, Perivolioti E, Idone FA, Motos A, Chiurazzi C, Travierso C, Fernández-Barat L, Amaro R, Hua Y, Ranzani OT, Bobi Q, Rigol M, Pratikaki M, Torres A, Fernández IF, Soler EA, de Vera APR, Pastor EE, Hernandis V, Ros Martínez J, Rubio RJ, Torner MM, Brugger SC, Vrettou C, Eroles AA, Moles SI, Cabello JT, Schoenenberger JA, Casals XN, Vidal MV, Garrido BB, Martinez MP, Mirabella L, Cotoia A, Giannopoulos A, Tullo L, Stella A, Di Bello F, Di Gregorio A, Dambrosio M, Cinnella G, Rosario LEDLC, Lesmes SPG, Romero JCG, Herrera ANG, Zakynthinos S, Pertuz EDD, Sánchez MJG, Sanz ER, Hualde JB, Hernández AA, Ramirez JR, Takahashi H, Kazutoshi F, Okada Y, Oobayashi W, Routsi C, Naito T, Baidya DK, Maitra S, Anand RK, Ray BR, Arora MK, Ruffini C, Rota L, Corona A, Sesana G, Atchade E, Ravasi S, Catena E, Naumann DN, Mellis C, Husheer SL, Bishop J, Midwinter MJ, Hutchings S, Corradi F, Brusasco C, Houzé S, Manca T, Ramelli A, Lattuada M, Nicolini F, Gherli T, Vezzani A, Young A, Carmona AF, Santiago AI, Guillamon LN, Jean-Baptiste S, Delgado MJG, Delgado-Amaya M, Curiel-Balsera E, Rivera-Romero L, Castillo-Lorente E, Carrero-Gómez F, Aguayo-DeHoyos E, Healey AJ, Cameron C, Jiao L, Thabut G, Stümpfle R, Pérez A, Martin S, del Moral OL, Toval S, Rico J, Aldecoa C, Oguzhan K, Demirkiran O, Kirman M, Genève C, Bozbay S, Kosuk ME, Asyralyyeva G, Dilek M, Duzgun M, Telli S, Aydin M, Yilmazer F, Hodgson LE, Dimitrov BD, Tanaka S, Stubbs C, Forni LG, Venn R, Vedage D, Shawaf S, Naran P, Sirisena N, Kinnear J, Dimitrov BD, Hodgson LE, Lortat-Jacob B, Stubbs C, Forni LG, Venn R, Londoño JG, Cardenas CL, Ginés AS, Gubianas CM, Sánchez EC, Sirvent JM, Panafidina V, Augustin P, Shlyk I, Ilyina V, Judickas S, Kezyte G, Urbanaviciute I, Serpytis M, Gaizauskas E, Sipylaite J, Sprung CL, Munteanu G, Desmard M, Morales RC, Kasdan H, Volker T, Reiter A, Cohen Y, Himmel Y, Meissonnier J, Banderas-Bravo ME, Gómez-Jiménez C, García-Martínez MV, Montravers P, Martínez-Carmona JF, Fernández-Ortega JF, O‘Dwyer MJ, Starczewska M, Wilks M, Vincent JL, Torsvik M, Gustad LT, Bangstad IL, Vinje LJ, de Molina FJG, Damås JK, Solligård E, Mehl A, Tsunoda M, Kang M, Saito M, Saito N, Akizuki N, Namiki M, Takeda M, Barbadillo S, Yuzawa J, Yaguchi A, Frantzeskaki F, Tsirigotis P, Chondropoulos S, Paramythiotou E, Theodorakopoulou M, Stamouli M, Gkirkas K, Dimopoulou IK, Alejandro R, Makiko S, Tsunoda M, Kang M, Yuzawa J, Akiduki N, Namiki M, Takeda M, Yaguchi A, Preau S, Ambler M, Álvarez-Lerma F, Sigurta A, Saeed S, Singer M, Jochmans S, Chelly J, Vong LVP, Sy O, Serbource-Goguel J, Rolin N, Weyer CM, Vallés J, Abdallah RI, Adrie C, Vinsonneau C, Monchi M, Mayr U, Huber W, Karsten E, Lahmer T, Thies P, Henschel B, Catalán RM, Fischer G, Schmid RM, Ediboglu O, Ataman S, Naz I, Yaman G, Kirakli C, Su PL, Kou PS, Lin WC, Palencia E, Chen CW, Lozano JAB, Sánchez PC, Francioni JEB, Ferrón FR, Simón JMS, Riad Z, Mezidi M, Aublanc M, Perinel S, Jareño A, Lissonde F, Louf-Durier A, Yonis H, Tapponnier R, Richard JC, Louis B, Guérin C, Mezidi M, Yonis H, Aublanc M, Granada RM, Lissonde F, Louf-Durier A, Perinel S, Tapponnier R, Richard JC, Guérin C, Marmanidou K, Oikonomou M, Nouris C, Loizou C, Ignacio ML, Soilemezi E, Matamis D, Somhorst P, Gommers D, Hayashi K, Hirayama T, Yumoto T, Tsukahara K, Iida A, Nosaka N, Cui N, Sato K, Ugawa T, Nakao A, Ujike Y, Hirohata S, Mojoli F, Torriglia F, Giannantonio M, Orlando A, Bianzina S, Liu D, Tavazzi G, Mongodi S, Pozzi M, Iotti GA, Braschi A, Jansen D, Gadgil S, Doorduin J, Roesthuis L, van der Hoeven JG, Wang H, Heunks LMA, Chen GQ, Sun XM, He X, Yang YL, Shi ZH, Xu M, Zhou JX, Pereira SM, Tucci MR, Su L, Tonelotto BFF, Simoes CM, Morais CCA, Pompeo MS, Kay FU, Amato MBP, Vieira JE, Suzuki S, Mihara Y, Hikasa Y, Qiu H, Okahara S, Morimatsu H, Kwon HM, Moon YJ, Lee SH, Jung KW, Shin WJ, Jun IG, Song JG, Hwang GS, Li R, Lee S, Moon YJ, Kwon HM, Jung K, Shin WJ, Jun IG, Song JG, Hwang GS, Ramelli A, Manca T, Jaffal K, Corradi F, Brusasco C, Nicolini F, Gherli T, Brianti R, Fanzaghi P, Vezzani A, Tudor BA, Klaus DA, Lebherz-Eichinger D, Rouzé A, Lechner C, Schwarz C, Bodingbauer M, Seemann R, Kaczirek K, Fleischmann E, Roth GA, Krenn CG, Malyshev A, Sergey S, Poissy J, Yamaguchi Y, Nomura T, Yoshitake E, Idei M, Yoshida T, Takaki S, Yamaguchi O, Kaneko M, Goto T, Tencé N, Sendid B, Zaien I, Wolf M, Trouiller P, Jacobs FM, Kelly JM, Veigas P, Hollands S, Min A, Rizoli S, Robles CMC, Nseir S, de Oca Sandoval MAM, Tarabrin O, Gavrychenko D, Mazurenko G, Tarabrin P, Garcia IP, Martin AD, Mendez MC, orden VA, Noval RL, Paramythiotou E, McCue C, Gemmell L, MacKay A, Luján J, Villa P, Llorente B, Molina R, Alcázar L, Juanas CA, Rogero S, Rizos M, Pascual T, Cambronero JA, Almudévar PM, Domínguez JP, Carmona SA, Castañeda DP, Abellán AN, Lucendo AP, Pérez LP, Rivas RF, Frantzeskaki F, Sanz NM, Ramos JV, Villamizar PR, Javadpour S, Kalani N, Amininejad T, Jamali S, Sobhanian S, Laurent A, Bonnet M, Antoniadou A, Rigal R, Aslanian P, Hebert P, Capellier G, Contreras MRD, Mejías CR, Ruiz FCS, Lombardo MD, Perez JC, de Hoyos EA, Vourli S, Estella A, Viciana R, Fontaiña LP, Rico T, Madueño VP, Recuerda M, Fernández L, Sandiumenge A, Bonet S, Mazo C, Zerva L, Rubiera M, Ruiz-Rodríguez JC, Gracia RM, Espinel E, Pont T, Kotsopoulos A, Jansen N, Abdo WF, Gopcevic A, Gavranovic Z, Armaganidis A, Vucic M, Glogoski MZ, Penavic LV, Horvat A, Martin-Villen L, Egea-Guerero JJ, Revuelto-Rey J, Aldabo-Pallas T, Correa-Chamorro E, Gallego-Corpa AI, Riera J, Granados PRDPR, Faivre V, Wildenberg L, Huot B, Lukaszewicz AC, Simsir M, Mengelle C, Payen D, Sanz NM, Valbuena BL, Gottlieb J, de la Fuente MV, Almudena PM, Pérez LP, Carmona SA, Abellán AN, Simón IF, Muñoz JJR, Ramos JV, Carmona SA, Almudevar PM, Greer M, Abellan AN, Lucendo MAP, Perez LP, Dominguez JP, Rivas RF, Villamizar PR, Wee S, Ong C, Lau YH, Wong Y, Wiesner O, Banderas-Bravo ME, Olea-Jiménez V, Mora-Ordóñez JM, Gómez-Jiménez C, Muñoz-Muñoz JL, Vallejo-Báez J, Daga-Ruiz D, Lebrón-Gallardo M, Rialp G, Raurich JM, Martínez M, Morán I, Martín MC, Heras G, Mas A, Vallverdú I, Hraiech S, Bourenne J, Guervilly C, Forel JM, Adda M, Acuña M, Sylla P, Mouaci A, Gainnier M, Papazian L, Bauer PR, Kumbamu A, Wilson ME, Pannu JK, Egginton JS, Kashyap R, Rello J, Gajic O, Yoshihiro S, Sakuraya M, Hayakawa M, Hirata A, Kawamura N, Tsutui T, Yoshida K, Hashimoto Y, Chang CH, Welte T, Hu HC, Chiu LC, Hung CY, Li SH, Kao KC, Sibley S, Drover J, D’Arsigny C, Parker C, Howes D, Atchade E, Moffatt S, Erb J, Ilan R, Messenger D, Ball I, Boyd JG, Harrison M, Ridi S, Muscedere J, Andrade AH, Mignot T, Costa RC, Souza VA, Gonzalez V, Amorim V, Rolla F, Filho CACA, Miranda R, Atchasiri S, Buranavanich P, Wathanawatthu T, Houzé S, Suwanpasu S, Bureau C, Rolland-Debord C, Poitou T, Clavel M, Perbet S, Terzi N, Kouatchet A, Similowski T, Demoule A, Jean-Baptiste S, Diaz P, Nunes J, Escórcio S, Silva G, Chaves S, Jardim M, Câmara M, Fernandes N, Duarte R, Jardim JJ, Thabut G, Pereira CA, Nóbrega JJ, Chen CM, Lai CC, Cheng KC, Chou W, Lee SJ, Cha YS, Lee WY, Onodera M, Lortat-Jacob B, Nakataki E, Oto J, Imanaka H, Nishimura M, Khadjibaev A, Sabirov D, Rosstalnaya A, Akalaev R, Parpibaev F, Antonucci E, Tanaka S, Rossini P, Gandolfi S, Montini E, Orlando S, van Nes M, Karachi F, Hanekom S, Andrade AH, Pereira UV, Filho CACA, Augustin P, Costa RC, Parkin MSW, Moore M, Andrade AH, Costa RC, Carvalho KVS, Filho CACA, Min HJ, Kim HJ, Lee DS, Desmard M, Choi YY, Lee EY, Song I, Kim DJ, E YY, Kim JW, Park JS, Cho YJ, Lee JH, Suh JW, Montravers P, Jo YH, Kim KS, Lee YJ, Ferrero-Calleja J, Merino-Vega D, González-Jiménez AI, Sigcha MS, Hernández-Tejedor A, Martin-Vivas A, Gabán-Díez Á, Soussi S, Luna RRD, De la Calle-Pedrosa N, Temprano-Gómez I, Afonso-Rivero D, Pellin-Ariño JI, Algora-Weber A, Fumis RRL, Ferraz AB, Junior JMV, Kirca H, Dudoignon E, Cakin O, Unal M, Mutlu H, Ramazanoglu A, Cengiz M, Nicolini EA, Pelisson FGF, Nunes RS, da Silva SL, Carreira MM, Ferry A, Bellissimo-Rodrigues F, Ferez MA, Basile-Filho A, Chao HC, Chen CM, Chen L, Hravnak M, Clermont G, Pinsky M, Dubrawski A, Chaussard M, Varas JL, Montero RM, Sánchez-Elvira LA, Díaz PV, Delgado CP, Ruiz BL, Guerrero AP, Galache JAC, Sherif H, Hassanin H, Benyamina M, El Hossainy R, Samy W, Ly H, David H, Burtin P, Charpentier C, Barral M, Courant P, Fournel E, Gaide-Chevronnay L, Alanio A, Durand M, Albaladejo P, Payen JF, Chavanon O, Ortiz AB, Pozzebon S, Lheureux O, Brasseur A, Vincent JL, Creteur J, Touratier S, Taccone FS, Fumagalli F, Scala S, Affatato R, De Maglie M, Zani D, Novelli D, Marra C, Luciani A, De Zani D, Chaouat M, Luini M, Letizia T, Pravettoni D, Staszewsky L, Masson S, Belloli A, Di Giancamillo M, Scanziani E, Latini R, Ristagno G, Lafaurie M, Kye YC, Suh GJ, Kwon WY, Kim KS, Yu KM, Babini G, Ristagno G, Grassi L, Fumagalli F, Bendel S, Mimoun M, De Maglie M, Affatato R, Masson S, Latini R, Scanziani E, Reinikainen M, Skrifvars M, Kappler F, Blobner M, Schaller SJ, Mebazaa A, Roasio A, Costanzo E, Cardellino S, Iesu E, Cavicchi FZ, Fontana V, Nobile L, Vincent JL, Creteur J, Taccone FS, Legrand M, Park M, You KM, Suh GJ, Kwon WY, Ko SB, Kim KS, Xini A, Marca L, Lheureux O, Brasseur A, Sheils MA, Vincent JL, Creteur J, Taccone FS, Beane A, Thilakasiri MCKT, De Silva AP, Stephens T, Sigera CS, Athapattu P, Jayasinghe S, Patel C, Padeniya A, Haniffa R, Santiago AI, Sáez VC, Ruiz-Ruano RDLC, González AS, Kunze-Szikszay N, Wand S, Klapsing P, Wetz A, Mohankumar L, Heyne T, Schwerdtfeger K, Troeltzsch M, Bauer M, Quintel M, Moerer O, Cook DJ, Rutherford WB, Scales DC, Adhikari NK, Akhtar N, Cuthbertson BH, Suzuki T, Takei T, Fushimi K, Iwamoto M, Nakagawa S, Mendsaikhan N, Begzjav T, Lundeg G, Dünser MW, Noriega SKP, Romero DG, Cabrera JLS, Santana JDM, Padilla YS, Pérez HR, Torrent RL, Kleinpell R, Chouris I, Radu V, Stougianni M, Aldana NN, Lavrentieva A, Lagonidis D, Price RDT, Day A, Arora N, Henderson MA, Hickey S, Costa MIA, Carvalho JP, Gomes AA, León JLÁ, Mergulhão PJ, Chan KKC, Shum HP, Yan WW, Maghsoudi B, Tabei SH, Masjedi M, Sabetian G, Tabatabaei HR, Akbarzadeh A, Baquero JD, Saigal S, Pakhare A, Joshi R, Pattnaik SK, Ray B, Rousseau AF, Michel L, Bawin M, Cavalier E, Reginster JY, Bernal FF, Damas P, Bruyere O, Zhou JC, Cauwenberghs H, De Backer A, Neels H, Deblier I, Berghmans J, Himpe D, Barea-Mendoza JA, Ahmadnia E, Portillo IP, Fernández MV, Gigorro RG, Vela JLP, Mateos HM, Alves SC, Varas GM, Rodriguez-Biendicho A, Carreño ER, González JCM, Hadley JS, Yang JS, Chiang CH, Hung WT, Huang WC, Cheng CC, Lin KC, Lin SC, Chiou KR, Wann SR, Lin KL, Millar M, Kang PL, Mar GY, Liu CP, Zhou JC, Choi YJ, Yoon SZ, Gordillo-Brenes A, Fernandez-Zamora MD, Perez-Borrero L, Arias-Verdu MD, Hall D, Aguilar-Alonso E, Herruzo-Aviles A, Garcia-Delgado M, Hinojosa-Perez R, Curiel-Balsera E, Rivera-Fernandez R, Lesmes SPG, Rosario LEDLC, Hernández AA, Herrera ANG, Hewitt H, Sanz ER, Sánchez MJG, Hualde JB, Pascual OA, León JPT, Irazabal JMG, Pérez AG, Fernández PA, Amor LL, Albaiceta GM, Yasuda H, Lesmes SPG, Rosario LEDLC, Hernández AA, Sanz ER, Sánchez MJG, Calvo SA, Herrera ANG, Hualde JB, Pascual OA, León JPT, Sanui M, Corona A, Ruffini C, Spazzadeschi A, Marrazzo F, Gandola A, Sciurti R, Savi C, Catena E, Ke MW, Cheng CC, Komuro T, Huang WC, Chiang CH, Hung WT, Lin KC, Lin SC, Wann SR, Chiou KR, Tseng CJ, Kang PL, Mar GY, Kawano S, Liu CP, Bertini P, De Sanctis F, Guarracino F, Bertini P, Baldassarri R, Guarracino F, Buitinck SH, van der Voort PHJ, Oto J, Andoh K, Nakataki E, Tsunano Y, Izawa M, Tane N, Onodera M, Nishimura M, Ghosh S, Gupta A, De Gasperi A, Mazza E, Yamamoto H, Limuti R, Prosperi M, Bissenova N, Yergaliyeva A, Talan L, Yılmaz G, Güven G, Yoruk F, Altıntas ND, Mukherjee DN, Noda E, Agarwal LK, Mandal K, Palomar M, Balsera B, Vallverdu M, Martinez M, Garcia M, Castellana D, Lopez R, Barcenilla F, Hatakeyama J, Kaminsky GE, Carreño R, Escribá A, Fuentes M, Gálvez V, Del Olmo R, Nieto B, Vaquerizo C, Alvarez J, De la Torre MA, Saitou N, Torres E, Bogossian E, Nouer SA, Salgado DR, Brugger SC, Jiménez GJ, Torner MM, Vidal MV, Garrido BB, Casals XN, Okamoto H, Gaite FB, Cabello JT, Martínez MP, Doganci M, Izdes S, Besevli SG, Alkan A, Kayaaslan B, Ramírez CS, Balcázar LC, Kobayashi A, Santana MC, Viera MAH, Escalada SH, Vázquez CFL, Penichet SMM, Campelo FA, López MADLC, Santana PS, Santana SR, Repessé X, Takei T, Artiguenave M, Paktoris-Papine S, Espinasse F, Dinh A, El Sayed F, Charron C, Géri G, Vieillard-Baron A, Marmanidou K, Oikonomou M, Matsukubo S, Nouris C, Dimitroulakis K, Soilemezi E, Matamis D, Ferré A, Guillot M, Teboul JL, Lichtenstein D, Mézière G, Richard C, Rotzel HB, Monnet X, Pham T, Beduneau G, Schortgen F, Piquilloud L, Zogheib E, Jonas M, Grelon F, Runge I, Terzi N, Lázaro AS, Grangé S, Barberet G, Guitard PG, Frat JP, Constan A, Chrétien JM, Mancebo J, Mercat A, Richard JCM, Brochard L, Prada DA, Prīdāne S, Sabeļņikovs O, Mojoli F, Orlando A, Bianchi I, Torriglia F, Bianzina S, Pozzi M, Iotti GA, Braschi A, Gimillo MR, Beduneau G, Pham T, Schortgen F, Piquilloud L, Zogheib E, Jonas M, Grelon F, Runge I, Terzi N, Grangé S, Barinas OD, Barberet G, Guitard PG, Frat JP, Constan A, Chrétien JM, Mancebo J, Mercat A, Richard JCM, Brochard L, Kondili E, Cortes MLB, Psarologakis C, Kokkini S, Amargianitakis V, Babalis D, Chytas A, Chouvarda I, Vaporidi K, Georgopoulos D, Trapp O, Kalenka A, Franco JF, Mojoli F, Orlando A, Bianchi I, Torriglia F, Bianzina S, Pozzi M, Iotti GA, Braschi A, Lozano JAB, Sánchez PC, Roca JMS, Francioni JEB, Ferrón FR, Simón JMS, Spadaro S, Karbing DS, Gioia A, Moro F, Corte FD, Mauri T, Volta CA, Carratalá A, Rees SE, Petrova MV, Mohan R, Butrov AV, Beeharry SD, Vatsik MV, Sakieva FI, Gobert F, Yonis H, Tapponnier R, Gonçalves B, Fernandez R, Labaune MA, Burle JF, Barbier J, Vincent B, Cleyet M, Richard JC, Guérin C, Shinotsuka CR, Creteur J, Turon R, Taccone FS, Törnblom S, Nisula S, Vaara S, Poukkanen M, Andersson S, Pettilä V, Pesonen E, Xie Z, Liao X, Mendes A, Kang Y, Zhang J, Kubota K, Egi M, Mizobuchi S, Hegazy S, El-Keraie A, El Sayed E, El Hamid MA, Rodrigues NJ, Miranda F, Pereira M, Godinho I, Gameiro J, Neves M, Gouveia J, e Silva ZC, Lopes JA, Mckinlay J, Kostalas M, Kooner G, Mata PJ, Dudas G, Horton A, Kerr C, Karanjia N, Creagh-Brown B, Forni L, Yamazaki A, Ganuza MS, Molina JAM, Martinez FH, Cavalcanti D, Freile MTC, Fernandez NG, Travieso PM, Bandert A, Frithiof R, Lipcsey M, Smekal D, Schlaepfer P, Durovray JD, Plouhinec V, Melo N, Chiappa C, Bellomo R, Schneider AG, Mitchell S, Durrant J, Street H, Dunthorne E, Shears J, Caballero CH, Hutchison R, Lacerda P, Schwarze S, Ghabina S, Thompson E, Prowle JR, Kirwan CJ, Gonzalez CA, Pinto JL, Orozco V, Patiño JA, Garcia PK, Kurtz P, Contreras KM, Rodriguez P, Echeverri JE, Righy C, Rosario LEDLC, Lesmes SPG, Romero JCG, Herrera ANG, Pertuz EDD, Sánchez MJG, Sanz ER, Hualde JB, Hernández AA, Irazabal JMG, Spatenkova V, Bradac O, Suchomel P, Urli T, Lazzeri EH, Aspide R, Zanello M, Perez-Borrero L, Garcia-Alvarez JM, Arias-Verdu MD, Aguilar-Alonso E, Rivera-Fernandez R, Mora-Ordoñez J, De La Fuente-Martos C, Castillo-Lorente E, Guerrero-Lopez F, Lesmes SPG, Rosario LEDLC, Pertuz EDD, Hernández AA, Romero JCG, Sánchez MJG, Herrera ANG, Ramírez JR, Sanz ER, Hualde JB, León JPT, Navarro-Guillamón L, Cordovilla-Guardia S, Iglesias-Santiago A, Guerrero-López F, Fernández-Mondéjar E, Vidal A, Perez M, Juez A, Arias N, Colino L, Perez JL, Pérez H, Calpe P, Alcala MA, Robaglia D, Perez C, Lan SK, Cunha MM, Moreira T, Santos F, Lafuente E, Fernandes MJ, Silva JG, Rosario LEDLC, Lesmes SPG, Herrera ANG, Romero JCG, Pertuz EDD, Sánchez MJG, Sanz ER, Echeverría JGA, Hernández AA, Hualde JB, Podlepich V, Sokolova E, Alexandrova E, Lapteva K, Kurtz P, Shuinotsuka C, Rabello L, Vianna G, Reis A, Cairus C, Salluh J, Bozza F, Torres JCB, Araujo NJF, García-Olivares P, Keough E, Dalorzo M, Tang LK, De Sousa I, Díaz M, Marcos-Zambrano LJ, Guerrero JE, Gomez SEZ, Lopez GDH, Cuellar AIV, Nieto ORP, Gonzalez JAC, Bhasin D, Rai S, Singh H, Gupta O, Bhattal MK, Sampley S, Sekhri K, Nandha R, Aliaga FA, Olivares F, Appiani F, Farias P, Alberto F, Hernández A, Pons S, Sonneville R, Bouadma L, Neuville M, Mariotte E, Radjou A, Lebut J, Chemam S, Voiriot G, Dilly MP, Mourvillier B, Dorent R, Nataf P, Wolff M, Timsit JF, Ediboglu O, Ataman S, Ozkarakas H, Kirakli C, Vakalos A, Avramidis V, Obukhova O, Kurmukov IA, Kashiya S, Golovnya E, Baikova VN, Ageeva T, Haritydi T, Kulaga EV, Rios-Toro JJ, Perez-Borrero L, Aguilar-Alonso E, Arias-Verdu MD, Garcia-Alvarez JM, Lopez-Caler C, De La Fuente-Martos C, Rodriguez-Fernandez S, Sanchez-Orézzoli MG, Martin-Gallardo F, Nikhilesh J, Joshi V, Villarreal E, Ruiz J, Gordon M, Quinza A, Gimenez J, Piñol M, Castellanos A, Ramirez P, Jeon YD, Jeong WY, Kim MH, Jeong IY, Ahn MY, Ahn JY, Han SH, Choi JY, Song YG, Kim JM, Ku NS, Shah H, Kellner F, Rezai F, Mistry N, Yodice P, Ovnanian V, Fless K, Handler E, Alejos RM, Romeu JDM, Antón DG, Quinart A, Martí AT, Llaurado-Serra M, Lobo-Civico A, Ventura-Rosado A, Piñol-Tena A, Pi-Guerrero M, Paños-Espinosa C, Peralvo-Bernat M, Marine-Vidal J, Gonzalez-Engroba R, Montesinos-Cerro N, Treso-Geira M, Valeiras-Valero A, Martinez-Reyes L, Sandiumenge A, Jimenez-Herrera MF, Helyar S, Riozzi P, Noon A, Hallows G, Cotton H, Keep J, Hopkins PA, Taggu A, Renuka S, Sampath S, Rood PJT, Frenzel T, Verhage R, Bonn M, Pickkers P, van der Hoeven JG, van den Boogaard M, Corradi F, Melnyk L, Moggia F, Pienovi R, Adriano G, Brusasco C, Mariotti L, Lattuada M, Bloomer MJ, Coombs M, Ranse K, Endacott R, Maertens B, Blot K, Blot S, Amerongen MPVN, van der Heiden ES, Twisk JWR, Girbes ARJ, Spijkstra JJ, Riozzi P, Helyar S, Cotton H, Hallows G, Noon A, Bell C, Peters K, Feehan A, Keep J, Hopkins PA, Churchill K, Hawkins K, Brook R, Paver N, Endacott R, Maistry N, van Wijk A, Rouw N, van Galen T, Evelein-Brugman S, Taggu A, Krishna B, Sampath S, Putzu A, Fang M, Berto MB, Belletti A, Cassina T, Cabrini L, Mistry M, Alhamdi Y, Welters I, Abrams ST, Toh CH, Han HS, Gil EM, Lee DS, Park CM, Winder-Rhodes S, Lotay R, Doyle J, Ke MW, Huang WC, Chiang CH, Hung WT, Cheng CC, Lin KC, Lin SC, Chiou KR, Wann SR, Shu CW, Kang PL, Mar GY, Liu CP, Dubó S, Aquevedo A, Jibaja M, Berrutti D, Labra C, Lagos R, García MF, Ramirez V, Tobar M, Picoita F, Peláez C, Carpio D, Alegría L, Hidalgo C, Godoy K, Bakker J, Hernández G, Sadamoto Y, Katabami K, Wada T, Ono Y, Maekawa K, Hayakawa M, Sawamura A, Gando S, Marin-Mateos H, Perez-Vela JL, Garcia-Gigorro R, Peiretti MAC, Lopez-Gude MJ, Chacon-Alves S, Renes-Carreño E, Montejo-González JC, Parlevliet KL, Touw HRW, Beerepoot M, Boer C, Elbers PWG, Tuinman PR, Abdelmonem SA, Helmy TA, El Sayed I, Ghazal S, Akhlagh SH, Masjedi M, Hozhabri K, Kamali E, Zýková I, Paldusová B, Sedlák P, Morman D, Youn AM, Ohta Y, Sakuma M, Bates D, Morimoto T, Su PL, Chang WY, Lin WC, Chen CW, Facchin F, Zarantonello F, Panciera G, De Cassai A, Venrdramin A, Ballin A, Tonetti T, Persona P, Ori C, Del Sorbo L, Rossi S, Vergani G, Cressoni M, Chiumello D, Chiurazzi C, Brioni M, Algieri I, Tonetti T, Guanziroli M, Colombo A, Tomic I, Colombo A, Crimella F, Carlesso E, Gasparovic V, Gattinoni L, Neto AS, Schmidt M, Pham T, Combes A, de Abreu MG, Pelosi P, Schultz MJ, Katira BH, Engelberts D, Giesinger RE, Ackerley C, Yoshida T, Zabini D, Otulakowski G, Post M, Kuebler WM, McNamara PJ, Kavanagh BP, Pirracchio R, Rigon MR, Carone M, Chevret S, Annane D, Eladawy S, El-Hamamsy M, Bazan N, Elgendy M, De Pascale G, Vallecoccia MS, Cutuli SL, Di Gravio V, Pennisi MA, Conti G, Antonelli M, Andreis DT, Khaliq W, Singer M, Hartmann J, Harm S, Carmona SA, Almudevar PM, Abellán AN, Ramos JV, Pérez LP, Valbuena BL, Sanz NM, Simón IF, Arrigo M, Feliot E, Deye N, Cariou A, Guidet B, Jaber S, Leone M, Resche-Rigon M, Baron AV, Legrand M, Gayat E, Mebazaa A, Balik M, Kolnikova I, Maly M, Waldauf P, Tavazzi G, Kristof J, Herpain A, Su F, Post E, Taccone F, Vincent JL, Creteur J, Lee C, Hatib F, Jian Z, Buddi S, Cannesson M, Fileković S, Turel M, Knafelj R, Gorjup V, Stanić R, Gradišek P, Cerović O, Mirković T, Noč M, Tirkkonen J, Hellevuo H, Olkkola KT, Hoppu S, Lin KC, Hung WT, Chiang CC, Huang WC, Juan WC, Lin SC, Cheng CC, Lin PH, Fong KY, Hou DS, Kang PL, Wann SR, Chen YS, Mar GY, Liu CP, Paul M, Bougouin W, Geri G, Dumas F, Champigneulle B, Legriel S, Charpentier J, Mira JP, Sandroni C, Cariou A, Zimmerman J, Sullivan E, Noursadeghi M, Fox B, Sampson D, McHugh L, Yager T, Cermelli S, Seldon T, Bhide S, Brandon RA, Brandon RB, Zwaag J, Beunders R, Pickkers P, Kox M, Gul F, Arslantas MK, Genc D, Zibandah N, Topcu L, Akkoc T, Cinel I, Greco E, Lauretta MP, Andreis DT, Singer M, Garcia IP, Cordero M, Martin AD, Pallás TA, Montero JG, Rey JR, Malo LR, Montoya AAT, Martinez ADCA, Ayala LYD, Zepeda EM, Granillo JF, Sanchez JA, Alejo GC, Cabrera AR, Montenegro AP, Pham T, Beduneau G, Schortgen F, Piquilloud L, Zogheib E, Jonas M, Grelon F, Runge I, Terzi N, Grangé S, Barberet G, Guitard PG, Frat JP, Constan A, Chrétien JM, Mancebo J, Mercat A, Richard JCM, Brochard L, Soilemezi E, Koco E, Savvidou S, Nouris C, Matamis D, Di Mussi R, Spadaro S, Volta CA, Mariani M, Colaprico A, Antonio C, Bruno F, Grasso S, Rodriguez A, Martín-Loeches I, Díaz E, Masclans JR, Gordo F, Solé-Violán J, Bodí M, Avilés-Jurado FX, Trefler S, Magret M, Reyes LF, Marín-Corral J, Yebenes JC, Esteban A, Anzueto A, Aliberti S, Restrepo MI, Larsson JS, Redfors B, Ricksten SE, Haines R, Powell-Tuck J, Leonard H, Ostermann M, Berthelsen RE, Itenov TS, Perner A, Jensen JU, Ibsen M, Jensen AEK, Bestle MH, Bucknall T, Dixon J, Boa F, MacPhee I, Philips BJ, Doyle J, Saadat F, Samuels T, Huddart S, McCormick B, DeBrunnar R, Preece J, Swart M, Peden C, Richardson S, Forni L, Kalfon P, Baumstarck K, Estagnasie P, Geantot MA, Berric A, Simon G, Floccard B, Signouret T, Boucekine M, Fromentin M, Nyunga M, Sossou A, Venot M, Robert R, Follin A, Renault A, Garrouste M, Collange O, Levrat Q, Villard I, Thévenin D, Pottecher J, Patrigeon RG, Revel N, Vigne C, Mimoz O, Auquier P, Pawar S, Jacques T, Deshpande K, Pusapati R, Wood B, Pulham RA, Wray J, Brown K, Pierce C, Nadel S, Ramnarayan P, Azevedo JR, Montenegro WS, Rodrigues DP, Sousa SC, Araujo VF, Leitao AL, Prazeres PH, Mendonca AV, Paula MP, Das Neves A, Loudet CI, Busico M, Vazquez D, Villalba D, Lischinsky A, Veronesi M, Emmerich M, Descotte E, Juliarena A, Bisso MC, Grando M, Tapia A, Camargo M, Ulla DV, Corzo L, dos Santos HP, Ramos A, Doglia JA, Estenssoro E, Carbonara M, Magnoni S, Donald CLM, Shimony JS, Conte V, Triulzi F, Stretti F, Macrì M, Snyder AZ, Stocchetti N, Brody DL, Podlepich V, Shimanskiy V, Savin I, Lapteva K, Chumaev A, Tjepkema-Cloostermans MC, Hofmeijer J, Beishuizen A, Hom H, Blans MJ, van Putten MJAM, Longhi L, Frigeni B, Curinga M, Mingone D, Beretta S, Patruno A, Gandini L, Vargiolu A, Ferri F, Ceriani R, Rottoli MR, Lorini L, Citerio G, Pifferi S, Battistini M, Cordolcini V, Agarossi A, Di Rosso R, Ortolano F, Stocchetti N, Lourido CM, Cabrera JLS, Santana JDM, Alzola LM, del Rosario CG, Pérez HR, Torrent RL, Eslami S, Dalhuisen A, Fiks T, Schultz MJ, Hanna AA, Spronk PE, Wood M, Maslove D. ESICM LIVES 2016: part three. Intensive Care Med Exp 2016. [PMCID: PMC5042925 DOI: 10.1186/s40635-016-0100-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
21
|
Tello-Ruiz MK, Stein J, Wei S, Preece J, Olson A, Naithani S, Amarasinghe V, Dharmawardhana P, Jiao Y, Mulvaney J, Kumari S, Chougule K, Elser J, Wang B, Thomason J, Bolser DM, Kerhornou A, Walts B, Fonseca NA, Huerta L, Keays M, Tang YA, Parkinson H, Fabregat A, McKay S, Weiser J, D'Eustachio P, Stein L, Petryszak R, Kersey PJ, Jaiswal P, Ware D. Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res 2015; 44:D1133-40. [PMID: 26553803 PMCID: PMC4702844 DOI: 10.1093/nar/gkv1179] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 10/13/2015] [Indexed: 12/21/2022] Open
Abstract
Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼ 200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials.
Collapse
Affiliation(s)
| | - Joshua Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Vindhya Amarasinghe
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Palitha Dharmawardhana
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Yinping Jiao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joseph Mulvaney
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - James Thomason
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Daniel M Bolser
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Arnaud Kerhornou
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Brandon Walts
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Nuno A Fonseca
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Laura Huerta
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Maria Keays
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Y Amy Tang
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Helen Parkinson
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Antonio Fabregat
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Sheldon McKay
- Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto, M5G 1L7, Canada
| | - Joel Weiser
- Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto, M5G 1L7, Canada
| | - Peter D'Eustachio
- Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Lincoln Stein
- Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto, M5G 1L7, Canada
| | - Robert Petryszak
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Paul J Kersey
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
| |
Collapse
|
22
|
Lingutla NT, Preece J, Todorovic S, Cooper L, Moore L, Jaiswal P. AISO: Annotation of Image Segments with Ontologies. J Biomed Semantics 2014; 5:50. [PMID: 25584184 PMCID: PMC4290088 DOI: 10.1186/2041-1480-5-50] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 11/26/2014] [Indexed: 01/24/2023] Open
Abstract
Background Large quantities of digital images are now generated for biological collections, including those developed in projects premised on the high-throughput screening of genome-phenome experiments. These images often carry annotations on taxonomy and observable features, such as anatomical structures and phenotype variations often recorded in response to the environmental factors under which the organisms were sampled. At present, most of these annotations are described in free text, may involve limited use of non-standard vocabularies, and rarely specify precise coordinates of features on the image plane such that a computer vision algorithm could identify, extract and annotate them. Therefore, researchers and curators need a tool that can identify and demarcate features in an image plane and allow their annotation with semantically contextual ontology terms. Such a tool would generate data useful for inter and intra-specific comparison and encourage the integration of curation standards. In the future, quality annotated image segments may provide training data sets for developing machine learning applications for automated image annotation. Results We developed a novel image segmentation and annotation software application, “Annotation of Image Segments with Ontologies” (AISO). The tool enables researchers and curators to delineate portions of an image into multiple highlighted segments and annotate them with an ontology-based controlled vocabulary. AISO is a freely available Java-based desktop application and runs on multiple platforms. It can be downloaded at http://www.plantontology.org/software/AISO. Conclusions AISO enables curators and researchers to annotate digital images with ontology terms in a manner which ensures the future computational value of the annotated images. We foresee uses for such data-encoded image annotations in biological data mining, machine learning, predictive annotation, semantic inference, and comparative analyses.
Collapse
Affiliation(s)
- Nikhil Tej Lingutla
- School of Electrical Engineering and Computer Science, Kelley Engineering Center, Oregon State University, Corvallis, OR 97331-2902 USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Sinisa Todorovic
- School of Electrical Engineering and Computer Science, Kelley Engineering Center, Oregon State University, Corvallis, OR 97331-2902 USA
| | - Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Laura Moore
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| |
Collapse
|
23
|
Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P. De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. PLoS One 2014; 9:e96855. [PMID: 24821410 PMCID: PMC4018402 DOI: 10.1371/journal.pone.0096855] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 04/12/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. PRINCIPAL FINDINGS The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ∼90% of these transcripts from each accession to barley and ∼95% of the transcripts to T. urartu genomes. However, only ∼77% transcripts mapped to the annotated barley genes and ∼85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ∼500,000 single nucleotide polymorphism (SNP) and ∼22,000 simple sequence repeat (SSR) sites. CONCLUSIONS De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers.
Collapse
Affiliation(s)
- Samuel E. Fox
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Mamatha Hanumappa
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Chris Sullivan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Vijay K. Tiwari
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Jeffrey M. Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - Abigail Sage
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Cathy Gresham
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Arnaud Kerhornou
- European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Dan Bolser
- European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Fiona McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Paul Kersey
- European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Gerard R. Lazo
- USDA-ARS, Western Regional Research Center, Albany, California, United States of America
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| |
Collapse
|
24
|
Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D'Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D. Gramene 2013: comparative plant genomics resources. Nucleic Acids Res 2013; 42:D1193-9. [PMID: 24217918 PMCID: PMC3964986 DOI: 10.1093/nar/gkt1110] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Whole-genome alignments complemented by phylogenetic gene family trees help infer syntenic and orthologous relationships. Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts. The pathways section also hosts 10 species-specific metabolic pathways databases developed in-house or by our collaborators using Pathway Tools software, which facilitates searches for pathway, reaction and metabolite annotations, and allows analyses of user-defined expression datasets. Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species. We continue to provide genetic and QTL maps and marker datasets developed by crop researchers. The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology.
Collapse
Affiliation(s)
- Marcela K Monaco
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto M5G 1L7, Canada, Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA and NAA Plant, Soil & Nutrition Laboratory Research Unit, USDA-ARS, Ithaca, NY 14853, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Maskell PD, Seetohul LN, Livingstone AC, Cockburn AK, Preece J, Pounder DJ. Stability of 3,4-Methylenedioxymethampetamine (MDMA), 4-Methylmethcathinone (Mephedrone) and 3-Trifluromethylphenylpiperazine (3-TFMPP) in Formalin Solution. J Anal Toxicol 2013; 37:440-6. [DOI: 10.1093/jat/bkt051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
26
|
Hanumappa M, Preece J, Elser J, Nemeth D, Bono G, Wu K, Jaiswal P. WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. Rice (N Y) 2013; 6:14. [PMID: 24280312 PMCID: PMC4883732 DOI: 10.1186/1939-8433-6-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 05/22/2013] [Indexed: 05/29/2023]
Abstract
BACKGROUND Next-generation sequencing and 'omics' platforms are used extensively in plant biology research to unravel new genomes and study their interactions with abiotic and biotic agents in the growth environment. Despite the availability of a large and growing number of genomic data sets, there are only limited resources providing highly-curated and up-to-date metabolic and regulatory networks for plant pathways. RESULTS Using PathVisio, a pathway editor tool associated with WikiPathways, we created a gene interaction network of 430 rice (Oryza sativa) genes involved in the seed development process by curating interactions reported in the published literature. We then applied an InParanoid-based homology search to these genes and used the resulting gene clusters to identify 351 Arabidopsis thaliana genes. Using this list of homologous genes, we constructed a seed development network in Arabidopsis by processing the gene list and the rice network through a Perl utility software called Pathway GeneSWAPPER developed by us. In order to demonstrate the utility of these networks in generating testable hypotheses and preliminary analysis prior to more in-depth downstream analysis, we used the expression viewer and statistical analysis features of PathVisio to analyze publicly-available and published microarray gene expression data sets on diurnal photoperiod response and the seed development time course to discover patterns of coexpressed genes found in the rice and Arabidopsis seed development networks. These seed development networks described herein, along with other plant pathways and networks, are freely available on the plant pathways portal at WikiPathways (http://plants.wikipathways.org). CONCLUSION In collaboration with the WikiPathways project we present a community curation and analysis platform for plant biologists where registered users can freely create, edit, share and monitor pathways supported by published literature. We describe the curation and annotation of a seed development network in rice, and the projection of a similar, gene homology-based network in Arabidopsis. We also demonstrate the utility of the Pathway GeneSWAPPER (PGS) application in saving valuable time and labor when a reference network in one species compiled in GPML format is used to project a similar network in another species based on gene homology.
Collapse
Affiliation(s)
- Mamatha Hanumappa
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Denise Nemeth
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Gina Bono
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Kenny Wu
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902 USA
| |
Collapse
|
27
|
Fox SE, Preece J, Kimbrel JA, Marchini GL, Sage A, Youens-Clark K, Cruzan MB, Jaiswal P. Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae). Appl Plant Sci 2013; 1:apps.1200011. [PMID: 25202520 PMCID: PMC4105277 DOI: 10.3732/apps.1200011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/07/2013] [Indexed: 05/03/2023]
Abstract
UNLABELLED PREMISE OF THE STUDY We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. • METHODS AND RESULTS More than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis), 104,950 (Spain), and 177,682 (Greece) transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum. The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium sylvaticum sequence reads aligned against the Bd21 genome revealed 394,654 single-nucleotide polymorphisms (SNPs) and >20,000 simple sequence repeat (SSR) DNA sites. • CONCLUSIONS To our knowledge, this is the first report of transcriptome sequencing of invasive plant species with a closely related sequenced reference genome. The sequences and identified SNP variant and SSR sites will provide tools for developing novel genetic markers for use in genotyping and characterization of invasive behavior of B. sylvaticum.
Collapse
Affiliation(s)
- Samuel E. Fox
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331 USA
| | - Justin Preece
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331 USA
| | - Jeffrey A. Kimbrel
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Fourth Floor, Emeryville, California 94608 USA
| | - Gina L. Marchini
- Department of Biology, Portland State University, Portland, Oregon 97201 USA
| | - Abigail Sage
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331 USA
| | - Ken Youens-Clark
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 USA
| | - Mitchell B. Cruzan
- Department of Biology, Portland State University, Portland, Oregon 97201 USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331 USA
| |
Collapse
|
28
|
Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, Jaiswal P. The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol 2013; 54:e1. [PMID: 23220694 PMCID: PMC3583023 DOI: 10.1093/pcp/pcs163] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.
Collapse
Affiliation(s)
- Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA
- These authors contributed equally to this work
- These authors contributed equally to the development of the Plant Ontology
| | - Ramona L. Walls
- New York Botanical Garden, 2900 Southern Blvd., Bronx, NY 10458-5126, USA
- These authors contributed equally to this work
- These authors contributed equally to the development of the Plant Ontology
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA
- These authors contributed equally to the development of the Plant Ontology
| | - Maria A. Gandolfo
- L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, 412 Mann Library Building, Ithaca, NY 14853, USA
- These authors contributed equally to the development of the Plant Ontology
| | - Dennis W. Stevenson
- New York Botanical Garden, 2900 Southern Blvd., Bronx, NY 10458-5126, USA
- These authors contributed equally to the development of the Plant Ontology
| | - Barry Smith
- Department of Philosophy, University at Buffalo, 126 Park Hall, Buffalo, NY 14260, USA
- These authors contributed equally to the development of the Plant Ontology
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA
| | - Balaji Athreya
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA
| | - Christopher J. Mungall
- Berkeley Bioinformatics Open-Source Projects, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720, USA
| | - Stefan Rensing
- Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Manuel Hiss
- Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany
- FRIAS - Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg, Germany
| | - Tanya Z. Berardini
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Donghui Li
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Eva Huala
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Mary Schaeffer
- Agriculture Research Services, United States Department of Agriculture, Columbia, MO 65211, USA
- Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA
| | - Naama Menda
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 148533, USA
| | - Elizabeth Arnaud
- Bioversity International, via dei Tre Denari, 174/a, Maccarese, Rome, Italy
| | - Rosemary Shrestha
- Genetic Resources Program, Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT), Apdo. Postal 6-641, 06600 Mexico, D.F., Mexico
| | - Yukiko Yamazaki
- Center for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka, 411-8540 Japan
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA
- These authors contributed equally to the development of the Plant Ontology
- *Corresponding author: E-mail,: ; Fax, +1-541-737-3573
| |
Collapse
|
29
|
Walls RL, Athreya B, Cooper L, Elser J, Gandolfo MA, Jaiswal P, Mungall CJ, Preece J, Rensing S, Smith B, Stevenson DW. Ontologies as integrative tools for plant science. Am J Bot 2012; 99:1263-75. [PMID: 22847540 PMCID: PMC3492881 DOI: 10.3732/ajb.1200222] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
PREMISE OF THE STUDY Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web. METHODS This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). KEY RESULTS Ontologies can advance plant science in four keys areas: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education. CONCLUSIONS Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies.
Collapse
Affiliation(s)
- Ramona L. Walls
- New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458-5126 USA
| | - Balaji Athreya
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, Oregon 97331-2902 USA
| | - Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, Oregon 97331-2902 USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, Oregon 97331-2902 USA
| | - Maria A. Gandolfo
- L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, Oregon 97331-2902 USA
| | - Christopher J. Mungall
- Berkeley Bioinformatics Open-Source Projects, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 64-121, Berkeley, California 94720 USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, Oregon 97331-2902 USA
| | - Stefan Rensing
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Barry Smith
- Department of Philosophy, University at Buffalo, 126 Park Hall, Buffalo, New York 14260 USA
| | - Dennis W. Stevenson
- New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458-5126 USA
| |
Collapse
|
30
|
Smita S, Lenka SK, Katiyar A, Jaiswal P, Preece J, Bansal KC. QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice. Database (Oxford) 2011; 2011:bar037. [PMID: 21965557 PMCID: PMC3184618 DOI: 10.1093/database/bar037] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The QlicRice database is designed to host publicly accessible, abiotic stress responsive quantitative trait loci (QTLs) in rice (Oryza sativa) and their corresponding sequenced gene loci. It provides a platform for the data mining of abiotic stress responsive QTLs, as well as browsing and annotating associated traits, their location on a sequenced genome, mapped expressed sequence tags (ESTs) and tissue and growth stage-specific expressions on the whole genome. Information on QTLs related to abiotic stresses and their corresponding loci from a genomic perspective has not yet been integrated on an accessible, user-friendly platform. QlicRice offers client-responsive architecture to retrieve meaningful biological information—integrated and named ‘Qlic Search’—embedded in a query phrase autocomplete feature, coupled with multiple search options that include trait names, genes and QTL IDs. A comprehensive physical and genetic map and vital statistics have been provided in a graphical manner for deciphering the position of QTLs on different chromosomes. A convenient and intuitive user interface have been designed to help users retrieve associations to agronomically important QTLs on abiotic stress response in rice. Database URL:http://nabg.iasri.res.in:8080/qlic-rice/.
Collapse
Affiliation(s)
- Shuchi Smita
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India
| | | | | | | | | | | |
Collapse
|
31
|
Donovan K, Scott K, Somerton M, Preece J, Manickam M. Transient photocurrents in a charge transfer complex of trinitrofluorenone with a carbazole substituted discotic liquid crystal. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2005.09.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
32
|
Abstract
In the clinical governance era, self-education is not adequate training for nurses to carry out sharp debridement, which is a risky process. Specialist nurses in south-east London drew up a workable procedure for training and practice.
Collapse
|
33
|
Rudolf M, Rowland G, Das G, Gardiner S, Khan F, Krishnan V, Mylona F, Preece J, Omosigho C, Willey C, Williamson A. What's the use of Archimedes? Arch Dis Child 2002; 87:168-9; discussion 168-9. [PMID: 12138076 PMCID: PMC1719176 DOI: 10.1136/adc.87.2.168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- M Rudolf
- MMedSc in Child Health, Department of Paediatrics, Obstetrics and Gynaecology, University of Leeds, UK.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Thompson C, Kinmonth AL, Stevens L, Peveler RC, Stevens A, Ostler KJ, Pickering RM, Baker NG, Henson A, Preece J, Cooper D, Campbell MJ. Effects of a clinical-practice guideline and practice-based education on detection and outcome of depression in primary care: Hampshire Depression Project randomised controlled trial. Lancet 2000; 355:185-91. [PMID: 10675118 DOI: 10.1016/s0140-6736(99)03171-2] [Citation(s) in RCA: 276] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
BACKGROUND Depression is a major individual and public-health burden throughout the world and is managed mainly in primary care. The most effective strategy to reduce this burden has been believed to be education of primary-care practitioners. We tested this assumption by assessing the effectiveness of an educational programme based on a clinical-practice guideline in improving the recognition and outcome of primary-care depression. METHODS We carried out a randomised controlled trial in a representative sample of 60 primary-care practices (26% of the total) in an English health district. Education was delivered to practice teams and quality tested by feedback from participants and expert raters. The primary endpoints were recognition of depression, defined by the hospital anxiety and depression (HAD) scale, and clinical improvement. Analysis was by intention to treat. FINDINGS The education was well received by participants, 80% of whom thought it would change their management of patients with depression. 21409 patients were screened, of whom 4192 were classified as depressed by the HAD scale. The sensitivity of physicians to depressive symptoms was 39% in the intervention group and 36% in the control group after education (odds ratio 1.2 [95% CI 0.88-1.61]). The outcome of depressed patients as a whole at 6 weeks or 6 months after the assessment did not significantly improve. INTERPRETATION Although well received, this in-practice programme, which was designed to convey the current consensus on best practice for the care of depression, did not deliver improvements in recognition of or recovery from depression.
Collapse
Affiliation(s)
- C Thompson
- Department of Mental Health, University of Southampton, Royal South Hants Hospital, Brinton's Terrace, UK
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Abstract
King's College Hospital, London, is the first trust to implement total bed management (TBM) to assist in the reduction and prevention of pressure sores. TBM is a new concept, whereby the tissue viability, manual handling and therapy needs of the trust are met at reduced costs through a partnership with a contractor. The introduction of a large number of electric bed frames and foam mattress replacements, with the availability of dynamic pressure-relieving equipment and a service agreement, has led to an expected trust saving of 86,000 Pounds in 1998/1999 and 100,000 Pounds in 1999/2000 onwards. This article outlines the perceived benefits of this approach.
Collapse
|
36
|
|
37
|
Gantz BJ, Tyler RS, McCabe BF, Preece J, Lowder MW, Otto SR. Iowa cochlear implant clinical project: results with two single-channel cochlear implants and one multi-channel cochlear implant. Laryngoscope 1985; 95:443-9. [PMID: 3838565 DOI: 10.1288/00005537-198504000-00013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cochlear implants have become a realistic alternative for the management of profoundly deaf patients. A variety of implants with differing electrode designs and coding strategies have been developed by nine major implant centers around the world. Each center has their "star" patient, but objective comparisons between these different implant designs are unavailable. In order to determine the performance characteristics of the present generation of cochlear implants, comparison data are vital. We have developed an independent center where uniform objective comparisons of different cochlear implants can be performed longitudinally. This report will present results of nine patients implanted with three different cochlear implant prostheses. Four patients have been implanted with the Los Angeles (House) single-channel implant, three patients have received the Vienna (Hochmair) single-channel intracochlear device, and two patients have been implanted with the Melbourne (Clark) 21-channel unit. All patients have had 11 months or more of experience with their cochlear prostheses. The results of a comprehensive audiologic battery which includes audiovisual and environmental tasks are presented. All implants provide significant improvement in speechreading and sound awareness. The findings to date suggest that there is strong correlation between top-down cognitive processing (as reflected by lip reading skills) and performance with cochlear implants.
Collapse
|
38
|
Keenlyside RA, Smith DH, Hirst D, Zuckerman AJ, Preece J. The distribution and significance of hepatitis B surface antigen in a rural population in Kenya. Ann Trop Med Parasitol 1977; 71:167-77. [PMID: 869607 DOI: 10.1080/00034983.1977.11687175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A rural population in Kenya was studied and a prevalence of HBsAg of 5-0% and an antibody prevalence of 50% in HBsAg in negative subjects has been found; 1-2% of the negative subjects converted to positive over a six-month period. A group of HBsAg positive subjects was compared with a matched group of HBsAg negative controls clinically in liver function tests and past medical history. No statistically significant differences were found between the two groups and neither group had experienced in the past significantly more skin scarification, injections or illness with jaundice. Both ad and ay subtypes occurred in the population. This is an unexpected and important finding, which gives scope for further detailed epidemiological studies in this population.
Collapse
|
39
|
Farrow LJ, Lamb SG, Coghill NF, Lindon RL, Preece J, Zuckerman AJ, Stewart JS. Hepatitis B antigen in viral hepatitis in West London. Br Med J 1974; 3:83-6. [PMID: 4852256 PMCID: PMC1611092 DOI: 10.1136/bmj.3.5923.83] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
During the first 12 months of a total population survey 249 patients were seen with viral hepatitis. A total of 215 of these were tested for hepatitis B antigen (HB Ag) by radioimmunoassay and 32 (15%) were positive.More than five times as many men (27) as women (5) were HBAg positive and 19 of the men were between the ages of 20 and 39 years. There were only four drug addicts among those tested, two of whom were positive, as were two of the four patients who were tattooed.Sixty out of 86 children (under 15 years) were tested for HBAg and none was positive.
Collapse
|
40
|
|
41
|
Abstract
Serum and red cell folate levels and serum vitamin B(12) levels have been estimated in 33 normal controls; 34 epileptic outpatients, 19 of whom also suffered from psychiatric illness; 33 epileptic inpatients with psychiatric illness; and 30 non-epileptic inpatients with psychiatric illness. Significant lowering of serum folate and red cell folate levels was observed in epileptic patients with psychiatric illness, and a less significant fall in red cell folate levels was found in non-epileptic psychiatric patients. Serum folate levels less than 2·5 ng/ml. were found in two controls, seven outpatient epileptics, 29 inpatients, and 10 non-epileptic patients. Red cell folate levels less than 100 ng/ml. were found in two controls, nine outpatient epileptics, 23 inpatient epileptics, and seven non-epileptic patients. A significant correlation was found between serum and red cell folate values in control, epileptic, and non-epileptic patients. In the epileptic patients there was a significant association between low serum and red cell folate levels and the presence of psychiatric illness. The origin and possible significance of these findings are discussed.
Collapse
|
42
|
|
43
|
|
44
|
|