Metaphrase: An Aid to the Clinical Conceptualization and Formalization of Patient Problems in Healthcare Enterprises

Patient descriptors, or “problems,” such as “brain metastases of melanoma” are an effective way for caregivers to describe patients. But most problems, e.g., “cubital tunnel syndrome” or “ulnar nerve compression,” found in problem lists in an Electronic Medical Record (EMR) are not comparable computationally – in general, a computer cannot determine whether they describe the same or a related problem, or whether the user would have preferred “ulnar nerve compression syndrome.” Metaphrase is a scalable, middleware component designed to be accessed from problemmanager applications in EMR systems. In response to caregivers' informal descriptors it suggests potentially equivalent, authoritative, and more formally comparable descriptors. Metaphrase contains a clinical subset of the 1997 UMLS Metathesaurus and some 10,000 “problems” from the Mayo Clinic and Harvard Beth Israel Hospital. Word and term completion, spelling correction, and semantic navigation, all combine to ease the burden of problem conceptualization, entry and formalization.

Modulation of smooth muscle proliferation in rat carotid artery by platelet-derived mediators and fibroblast growth factor-2

Endothelial denuding injury to the rat carotid artery stimulates smooth muscle cell proliferation in the tunica media. Fibroblast growth factor-2 (FGF2) is responsible for a significant portion of this proliferation but other factors may contribute, particularly those released from adherent platelets. We therefore tested the effects of a range of platelet-derived factors. After filament injury, which minimises FGF2 release, the proliferation rate in thrombocytopaenic rats was decreased by 74% (P < 0.02). After balloon injury, antibody neutralisation of platelet-derived growth factor (PDGF) caused a 27% decrease in proliferation (P < 0.05), while inhibition of histamine H(1) receptors caused a 53% increase (P < 0.05). When filament injury was performed 1 h after FGF2 injection, the proliferation rate increased from 2.3+/-0.7 to 32.8+/-2.7% (P < 0.001), while filament injury alone caused a proliferation rate of only 18.3+/-2.9% (P < 0.01 versus filament plus FGF2). These data suggest that platelet-derived factors interact with FGF2 that is adsorbed to the vessel wall in the control of smooth muscle cell proliferation, and that the net effect of platelets is to stimulate smooth muscle cell proliferation. PDGF, but no other platelet agonist tested, contributes to that stimulation.

Phosphatidylinositol 3-kinase signaling is important for smooth muscle cell replication after arterial injury

The phosphoinositide 3-kinase [PI(3)K] pathway is a key signaling pathway important for replication of mammalian cells. In this study, we examined the role of PI(3)K in smooth muscle cell (SMC) replication after balloon catheter injury of rat carotid arteries. Protein kinase B (PKB), a downstream target of PI(3)K, was phosphorylated at 30 and 60 minutes after injury and to a lesser degree after 6 hours and 1 and 2 days but not after 7 days. Wortmannin (10 microgram per rat), a PI(3)K inhibitor, given to rats 60 and 5 minutes before and 11 hours after balloon injury, reduced the levels of phosphorylated PKB. SMC replication quantified between 24 to 48 hours was significantly reduced compared with control replication, as were the levels of cyclin D(1). Wortmannin was also administered to rats between days 7 and 8 and between days 7 and 9 after balloon catheter injury. A reduction in levels of phosphorylated PKB was detected, but no decrease in the replication of intimal SMCs was observed in either experiment. These data demonstrate that the PI(3)K signal transduction pathway plays an important role in medial but not intimal SMC replication.

Proliferation of intimal smooth muscle cells. Attenuation of basic fibroblast growth factor 2-stimulated proliferation is associated with increased expression of cell cycle inhibitors

Basic fibroblast growth factor (FGF2) is a potent mitogen for medial smooth muscle cells and is necessary for their proliferation after balloon catheter injury; however, intimal smooth muscle cells do not require FGF2 for their proliferation, and they respond only weakly to exogenous FGF2. The present study examined the activation of extracellular signal-regulated kinase (ERK) signaling as well as the expression and activity of cell cycle proteins in FGF2-stimulated intimal smooth muscle cells. FGF2 activates ERKs 1 and 2, and Western blot analysis showed that cyclin D, cyclin E, and cyclin-dependent kinase (CDKs) 2 and 4 were expressed in intimal smooth muscle cells after FGF2 infusion. FGF2 stimulation, however, did not lead to phosphorylation of the retinoblastoma protein (Rb), CDK 2 activation, or expression of cyclin A. Western blot analysis showed that intimal smooth muscle cells express elevated levels of the cell cycle inhibitors p15(INK4b) and p27(Kip1), compared with medial smooth muscle cells, and that FGF2 stimulation does not reduce the level of these inhibitors. These studies suggest that despite activation of ERKs 1 and 2 and expression of the cell cycle activators, cyclin D and cyclin E, high levels of cell cycle inhibitors may inhibit cell cycle transit in FGF2-stimulated intimal smooth muscle cells.

Metaphrase: an aid to the clinical conceptualization and formalization of patient problems in healthcare enterprises

Patient descriptors, or "problems," such as "brain metastases of melanoma" are an effective way for caregivers to describe patients. But most problems, e.g., "cubital tunnel syndrome" or "ulnar nerve compression," found in problem lists in an Electronic Medical Record (EMR) are not comparable computationally--in general, a computer cannot determine whether they describe the same or a related problem, or whether the user would have preferred "ulnar nerve compression syndrome." Metaphrase is a scalable, middleware component designed to be accessed from problem-manager applications in EMR systems. In response to caregivers' informal descriptors it suggests potentially equivalent, authoritative, and more formally comparable descriptors. Metaphrase contains a clinical subset of the 1997 UMLS Metathesaurus and some 10,000 "problems" from the Mayo Clinic and Harvard Beth Israel Hospital. Word and term completion, spelling correction, and semantic navigation, all combine to ease the burden of problem conceptualization, entry and formalization.

Cell replication in the arterial wall: activation of signaling pathway following in vivo injury

This study examined intracellular signal events of arterial cells following balloon catheter injury to rat carotid artery. Within 30 minutes, a marked increase in extracellular signal-regulated kinase-1/2 (ERK1/2) activity was observed. This activity remained elevated for 12 hours but had decreased to control levels by day 1. No increase in ERK1/2 was detected at any later times. Injection of anti-fibroblast growth factor 2 antibody (60 mg i.v.) significantly inhibited the activation of ERK1/2 at 30 minutes after the injury. PD98059 (80 micromol/L), a selective inhibitor of mitogen-activated protein kinase/ERK kinase-1 (MEK1), decreased ERK1/2 activity in injured arteries and also reduced the medial cell replication. In contrast, PD98059 did not block the intimal cell replication at day 8. Mitogen-activated protein kinase phosphatase-1 (MKP-1) was expressed within hours after injury but only weakly at later times; MKP-1 was again expressed after 7 and 14 days. The expression of MKP-1 was associated with an activation of c-Jun amino-terminal kinase. Injury to the arterial wall also stimulated the activity of p70 S6 kinase from 30 minutes to 12 hours, suggesting an alternative pathway in mitogenic signaling of early cell replication. These findings demonstrate that fibroblast growth factor 2-induced ERK1/2 activation promotes medial cell replication after balloon injury; however, signaling of intimal cell replication may not be linked to the MEK1-dependent ERK pathway.

Flight style of the black-billed magpie: variation in wing kinematics, neuromuscular control, and muscle composition

Black-billed magpies (Pica pica; Corvidae) exhibit an unusual flight style with pronounced, cyclic variation in wingbeat frequency and amplitude during level, cruising flight. In an effort to better understand the underlying internal mechanisms associated with this flight style, we studied muscle activity patterns, fiber composition of the pectoralis muscle, and wingbeat kinematics using both laboratory and field techniques. Over a wide range of speeds in a windtunnel (0-13.4 m s-1), wingbeat frequency, wingtip elevation, and relative intensity of electromyographic (EMG) signals s-1 from the flight muscles were least at intermediate speeds, and increased at both slower and faster speeds, in approximate agreement with theoretical models that predict a U-shaped curve of power output with flight speed. Considerable variation was evident in kinematic and electromyographic variables, but variation was continuous, and, thus, was not adequately described by the simple two-gait system which is currently accepted as describing gait selection during vertebrate flight. Indirect evidence suggests that magpies vary their flight style consistent with reducing average power costs in comparison to costs associated with continuous flapping at a fixed level of power per wingbeat. The range of variation for the kinematic variables was similar in the field and lab; however, in the field, proportionally fewer flights showed significant correlations between wingbeat frequency and the other variables. Average flight speed in the field was 8.0 m s-1. Average wingbeat frequency was less in the field than in the windtunnel, but mean values for wingtip elevation and wingspan at midupstroke were not significantly different. Histological study revealed that the pectoralis muscle of magpies contained only fast-twitch (acid-stable) muscle fibers, which were classified as red (R) and intermediate (I) based on oxidative and glycolytic capacities along with fiber diameter. This fiber composition may be related to variation in wingbeat kinematics, but such composition is found in the pectoralis of other bird species. This suggests that the muscle fibers commonly found in the pectoralis of small to medium sized birds are capable of a wider range of efficient contractile velocities than predicted by existing theory. Future studies should explore alternative explanations for variation in wingbeat kinematics, including the potential role of nonverbal communication among cospecifics.

Toward reusable software components at the point of care

An architecture built from five software components -a Router, Parser, Matcher, Mapper, and Server -fulfills key requirements common to several point-of-care information and knowledge processing tasks. The requirements include problem-list creation, exploiting the contents of the Electronic Medical Record for the patient at hand, knowledge access, and support for semantic visualization and software agents. The components use the National Library of Medicine Unified Medical Language System to create and exploit lexical closure-a state in which terms, text and reference models are represented explicitly and consistently. Preliminary versions of the components are in use in an oncology knowledge server.

MEME-II supports the cooperative management of terminology

Health care enterprises need enterprise-wide terminologies to compare, reuse and repurpose health care descriptions. But once they are created, these terminologies need to be maintained and enhanced to sustain their utility and that of the descriptions encoded with them. MEME II (Metathesaurus Enhancement and Maintenance Environment, Version II) supports the required activities and enables enterprises to leverage their investment in terminology and descriptions by permitting remote-extra-enterprise-enhancements to terminology to be incorporated locally, and local-intra-enterprise-enhancements to be shared remotely. MEME II represents all changes to terminologies as data, or "actions," that can be interpreted by an "action engine." These actions, or messages, represent semantic "units of work" that can be interpreted by other copies of MEME II. The exchange of update messages increases the likelihood that the comparability of terminology-based health care descriptions can be sustained.

Categorization of free-text problem lists: an effective method of capturing clinical data

Problem lists assist in organizing patient information in computer based medical records. However, in order to use problem lists for billing, research, decision support and standardization, a categorization of the problems entered is required. We describe the problem list component of our computerized patient record, the On-line Medical Record (OMR), which combines a free-text entry mechanism with a categorization scheme, using a dictionary containing 846 terms. All 118,040 problems entered during the system's six years of use have been analyzed, 477 clinicians have entered a mean +/- S.D. of 238 +/- 604 problems into 22,311 patient records. The average number of problems in each patient's file was 5.1 +/- 3.9. Comments were typed for 80,281 (68%) of the problems, ranging in length from 1 to 2456 characters, with a mean length of 98 +/- 110 characters. Half the problems were entered on the day of the encounter with the patient. Overall, 66% of all problems were categorized in relation to terms from the problem dictionary. Lexical analysis of all problem names showed that 80% could be mapped to Meta 1.4, Snomed 3.0 or a pre-release version of Read 3.0. We conclude that a problem list entry scheme combining free-text entry and optional categorization using a dictionary can result in a high proportion of problems being categorized as desired. Improvement of the system by elimination of unused dictionary terms and addition of 1000 terms identified by the lexical analysis is likely to result in even higher categorization rates.

Formal properties of the Metathesaurus

The Metathesaurus is a machine-created, human edited and enhanced synthesis of authoritative biomedical terminologies. Its formal properties permit it to be a) exploited by computers, and b) modified and enhanced without compromising that usage. If further constraints were imposed on the existence and identity of Metathesaurus relationships, i.e., if every Metathesaurus concept had a "genus" and a "differentia," then the Metathesaurus could be converted into an "Aristotelian Hierarchy." In this sense, a genus is a concept that classifies another concept, and a differentia is a concept that distinguishes the classified concept from all other concepts in the same class. Since, in principle, these constraints would make the Metathesaurus easier to leverage and maintain computationally, it is interesting to ask to what degree the maintenance and enhancement procedures now in place are producing a Metathesaurus that is also an "Aristotelian Hierarchy." Given a liberal interpretation of the current Metathesaurus schema, the proportion of the Metathesaurus that is "Aristotelian" in each annual version is increasing in spite of dramatic concurrent increases in the number of Metathesaurus concepts. Without formality there is no modifiability nor scalability. [1] We need formal methods and computer-based tools that can help us with the task [of controlled medical vocabulary construction]. We need research in which controlled vocabulary development is the focus rather than a stepping stone for work on other theories and applications. [2]

Recognizing new medical knowledge computationally

Can new medical knowledge be recognized computationally? We know knowledge is changing, and our knowledge-based systems will need to accommodate that change in knowledge on a regular basis if they are to stay successful. Computational recognition of these changes seems desirable. It is unlikely that low level objects in the computational universe, bits and characters, will change much over time, higher level objects of language, where meaning begins to emerge, may show change. An analysis of ten arbitrarily selected paragraphs from the Medical Knowledge Self-Assessment Program of the American College of Physicians was used as a test bed for nominal phrase recognition. While there were words not known to Meta-1.2, only 8 of the 32 concepts new to the primary author were pointed to by new words. Use of a barrier word method was successful in identifying 23 of the 32 new concepts. Use of co-occurrence (in sentences) of putative nominal phrases may reduce the amount of human effort involved in recognizing the emergence of new relationships.

Inhibition of smooth muscle cell proliferation in injured rat arteries. Interaction of heparin with basic fibroblast growth factor

Heparin inhibits smooth muscle cell (SMC) proliferation after arterial injury by mechanisms that have yet to be defined. Since the initiation of SMC proliferation is mediated by basic fibroblast growth factor (bFGF), we have investigated the possibility that heparin inhibits SMC proliferation by displacing bFGF from the arterial wall. Using a rat carotid artery model of balloon catheter injury, we demonstrate that a bolus injection of heparin depletes the arterial wall of both systemically administered bFGF and of endogenous bFGF. Heparin, however, does not reduce the bFGF content of unmanipulated arteries. Further, a single injection of heparin given at the time of balloon injury reduces SMC proliferation by 55% but has no effect when given 6 h after injury. SMC proliferation induced in a denuded artery by injection of bFGF is inhibited almost completely by a bolus injection of heparin; however, pretreatment with a bolus of heparin does not prevent SMC from responding to a subsequent bolus of bFGF. These experiments suggest that heparin can inhibit SMC proliferation in part by removal of released bFGF from sites of injury.

Intimal smooth muscle cell proliferation after balloon catheter injury. The role of basic fibroblast growth factor

The localization and synthesis of basic fibroblast growth factor (bFGF) in the rat carotid artery were investigated at times of chronic smooth muscle cell proliferation. Immunocytochemical staining showed the presence of bFGF in the uninjured arterial wall, and after balloon injury, this cellular staining was decreased. Western and northern blot analyses likewise showed that the amount of bFGF protein and mRNA decreased after injury. A neutralizing antibody to bFGF was administered 4 and 5 days after injury and was found to have no effect on intimal smooth muscle cell proliferation. These data suggest that an increase in the expression of bFGF is not necessary for chronic smooth muscle cell proliferation observed after balloon catheter injury and that bFGF is not the major mitogen responsible for intimal smooth muscle cell proliferation.

The semantic structure of the UMLS Metathesaurus

Meta-1.1, the UMLS metathesaurus, represents medical knowledge in the forms of names of concepts and links between those concepts. The representations of the semantic neighborhood of a concept can be thought of as dimensions of the property of semantic locality and include term information (broader, narrower, or otherwise related), the contextual information (parent-child, siblings in a hierarchy), the semantic types, and the co-occurrence data (links discovered empirically from concepts used to index the medical literature.) The degree of redundancy of each of these dimensions was investigated by reviewing the extent of multiple presentations of concepts which appear as related to a given concept. The degree of overlap was surprisingly small. While the co-occurrence data finds some of the links represented by other dimensions, those links are but minute fractions of the vast amount of co-occurrence derived links. Because parent-child relationships are often subsumptive (or categorical) in nature, it might be expected that siblings usually share the same semantic types. While true in the aggregate, the wide variance in percent of types shared may reflect the intended usages of the source vocabularies. Noun phrases were extracted from the definitions of 40 concepts in Meta-1 in order to assess systematically the coverage of important concepts by Meta-1, and to assess whether the links between these definitional concepts, which may have special value, and the concept being defined were indeed present. Out of 161 of these definitional concepts, 29 were not represented in Meta-1, and 37 of those represented in Meta-1 had no direct link to the concept they were defining.(ABSTRACT TRUNCATED AT 250 WORDS)

The Meta-1.2 engine: a refined strategy for linking biomedical vocabularies

This paper presents a preliminary description of the database schema and associated procedures that are the foundation for the "engine" that will produce Meta-1.2. Meta-1.2 is the next incarnation of the Metathesaurus, which is one of the principal components of the National Library of Medicine's Unified Medical Language System (UMLS). We use the word "engine" as a generic term that includes a database and the programs that operate on it. While this design builds heavily upon previous work, it incorporates some major changes in philosophy. A major hypothesis is that the simple representation described here is suitable for any controlled vocabulary in the biomedical domain. Indeed, this hypothesis is central to a strategy for producing future versions of the Metathesaurus and for supporting collaboration with people who wish to contribute additional terms and relationships to the Metathesaurus. Another change involves the representation of classes and relationships. The revised database schema includes an explicit representation of the source or "authority" for relationships, which is analogous to the way that the sources of terms have been represented since the first version of the Metathesaurus. A sequence of steps utilizing the new representations to produce the Metathesaurus is presented.

Biomedical database inter-connectivity: an experiment linking MIM, GENBANK, and META-1 via MEDLINE

The linkage of disparate biomedical databases is an important goal of the Unified Medical Language (UMLS) Project. We conducted an experiment to investigate the feasibility of using UMLS resources to link databases in clinical genetics and molecular biology. References from MIM ("Mendelian Inheritance in Man") were lexically mapped to the equivalent citations in MEDLINE. The MeSH major subject headings by which the citations in a particular MIM entry had been indexed were used to develop a "genetic-disorder-centered view of the world" in Meta-1 (the first official version of the UMLS Metathesaurus). Our hypothesis was that these MeSH subject headings could provide access to a "semantic neighborhood" in Meta-1 that would be relevant to a particular genetic disorder. By browsing in this "semantic neighborhood," a user could select various combinations of terms with which to search MEDLINE through an interface between Meta-1 and Grateful Med. Such searches might retrieve citations that were more recent than those in MIM or that provided useful supplementary information. Since some MEDLINE records contain pointers to entries in GENBANK, information about genetic sequences related to a particular clinical genetic disorder could also be retrieved. This scenario was implemented for a small number of MIM entries, providing a concrete demonstration that linking disparate electronic databases in an important subdomain of biomedicine is relatively straightforward.

Adding your terms and relationships to the UMLS Metathesaurus

The National Library of Medicine's Unified Medical Language System [1] Metathesaurus contains the richest single corpus of biomedical names in existence. Yet, developers wishing to make use of the Metathesaurus will be confronted by users who want to add local terminology and relationships not already represented there. We urge developers to fill those needs, while, at the same time, they plan for the many consequences of unilateral Metathesaurus enhancement. Foremost among these consequences is the need to maintain local enhancements across subsequent releases of the Metathesaurus. These problems are illustrated via examples of candidate Metathesaurus enhancement terms in use at the Columbia-Presbyterian Medical Center (CPMC), at the Mayo Clinic, and in Current Disease Descriptions (CDD). Sharing and reuse of Metathesaurus enhancement methods may permit local enhancements to be used at other sites, and it may permit the global Metathesaurus utilization effort to benefit from economies of scale.

From meaning to term: semantic locality in the UMLS Metathesaurus

The Unified Medical Language System Metathesaurus represents the results of a synthesis of existing biomedical naming systems (thesauri). The naming and other information about the meanings in the Metathesaurus can be used to find the preferred naming of that meaning in the source chosen by the user, by exploiting the property of semantic locality. The aspects of semantic locality in the Metathesaurus which can be thus exploited are the terms, the semantic types, the use of that term in a source context, and the co-occurrence of terms in MEDLINE. To find how a meaning is named in the source of choice, a user must exploit one of these aspects of semantic locality, entering a term somehow related to the term being sought, and navigating to the preferred term. While the first three of these aspects of semantic locality are normative, the last is empirical. Testing of the utility of the aspects of semantic locality in information retrieval would require a uniform interface with 1, no Metathesaurus, 2, the Metathesaurus without the aspects in question, and 3, the Metathesaurus including all the aspects. Other potential uses of empirically derived semantic locality include defining or suggesting potentially relevant concepts in a given situation.