David Sherertz - Academia.edu (original) (raw)

Papers by David Sherertz

The MUMPS programming system was designed and developed to facilitate shared conversational acces... more The MUMPS programming system was designed and developed to facilitate shared conversational access to a hierarchically-organized data base on a small computer. The MUMPS language, which has recently been standardized, contains features for numeric and string operations, along with a built-in file system called globals, embedded in a multiprogrammed execution environment. This paper gives an overview of the MUMPS language and a typical MUMPS system, then evaluates MUMPS in terms of modern notions of programming languages and software development. Despite the many attractive features for the development of interactive programs, MUMPS is seen to have a number of shortcomings when evaluated in this way. Among the problem areas are weakness of control structures, the ability to write self-modifying code, the incomprehensibility of most MUMPS programs, and the lack of support given by the language to notions of abstraction and modularity.

ACM Sigmini Newsletter, Mar 1, 1976

The MUMPS programming system was designed and developed to facilitate shared conversational acces... more The MUMPS programming system was designed and developed to facilitate shared conversational access to a hierarchically-organized data base on a small computer. The MUMPS language, which has recently been standardized, contains features for numeric and string operations, along with a built-in file system called globals, embedded in a multiprogrammed execution environment. This paper gives an overview of the MUMPS language and a typical MUMPS system, then evaluates MUMPS in terms of modern notions of programming languages and software development. Despite the many attractive features for the development of interactive programs, MUMPS is seen to have a number of shortcomings when evaluated in this way. Among the problem areas are weakness of control structures, the ability to write self-modifying code, the incomprehensibility of most MUMPS programs, and the lack of support given by the language to notions of abstraction and modularity.

Proceedings of the Annual Symposium on Computer Application in Medical Care, Nov 7, 1990

... Alexa T. McCray and William T. Hole ... The process of assigning semantic types to more than ... more ... Alexa T. McCray and William T. Hole ... The process of assigning semantic types to more than 30,000 concepts in the first version of the Metathesaurus (Meta-l), has led to a number of improvements to thepreliminary network described in [3]. These involved, primarily, changes to ...

PubMed, 1993

Can new medical knowledge be recognized computationally? We know knowledge is changing, and our k... more 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.

Proceedings of the Annual Symposium on Computer Application in Medical Care, Nov 7, 1990

The UMLS project seeks to provide a unified interface to biomedical knowledge resources. Patient ... more The UMLS project seeks to provide a unified interface to biomedical knowledge resources. Patient medical records are an enormous repository of clinical intervention and outcome, and are drawing increasing attention in the pursuit of quality assurance, outcomes research, and epidemiologic analysis. We sought to evaluate an unedited version of the preliminary UMLS Metathesaurus, Meta-1, for the automated coding of medical diagnosis and surgical procedures. Identical evaluations were undertaken using SNOMED and the Mayo Clinic indexing lexicon. Meta-1 performed comparably to the comparison clinical indexing systems, although all systems exhibited problems associated with clinical attribute levels and modifier combinations.

Proceedings of the Annual Symposium on Computer Application in Medical Care, Nov 7, 1990

One of three knowledge sources being developed as part of the mUm's Ems Project is a bimedical th... more One of three knowledge sources being developed as part of the mUm's Ems Project is a bimedical thesaurus, caled the Metathesaurus. The Metathesaurus contains inter-term relaionshgps across six bomedical nomenclaturs and classfiation systems, deivablefiom lexical mapping techniques. 7he first public version of the Metathesaurus, calledmErA-1, was built In two stages-fuist, source inversion and second, source matching. During the Sprin of 1989, "official" versions for the six sources were obtained In machine-readableform. Source spefic techniques were derived empiicaly to analyze the information structure and content of each source. The results of each analysis wre used to guide the "Inversio of the corresponding source, resulting in a homogeneous representation for all sowrces. The core concepts of META-1 come prmarilyfromMEDuN index terns (MesHO. Previous work on lexical mapping methodology developed algorithmic methods to link cncepts in d(f ferent sources. These methods were refined Iteratively, and used to Iplement a META-1 "!matching engine". The Initial version of META-i was constructed with this engine, by matching the MFrA-1 core concepts to the other sources. This version ofmETA-i was edited and enhanced by domain experts, after the Inclusion of supplemtay informai, to produce thefirst publicly released version ofMErA-1.

Proceedings of the Annual Symposium on Computer Application in Medical Care, Nov 4, 1981

RECONSIDER is an interactive computer program which produces a differential diagnosis given a lis... more RECONSIDER is an interactive computer program which produces a differential diagnosis given a list of patient attributes. The program's principal knowledge base is a corpus of 3,262 disease definitions represented in the form of structured natural language text. As these definitions were originally prepared for human use, RECONSIDER uses medical knowledge that is semantically identical to an information source that might be used by a physician. Thus, RECONSIDER can explain the inclusion of a particular disease in a differential by displaying the way in which the disease's definition relates to the list of patient attributes, and by ranking the strength of this relation relative to the rest of the differential. Use of RECONSIDER is illustrated on cases from the literature, and a case of pyruvate kinase deficiency (PK disease). Included for comparison are cases diagnosed by INTERNIST[1] and PIP[2], two well known diagnosis programs.

Proceedings of the Annual Symposium on Computer Application in Medical Care, Nov 7, 1990

Proceedings of the Annual Symposium on Computer Application in Medical Care, Nov 7, 1990

... Alexa T. McCray and William T. Hole ... The process of assigning semantic types to more than ... more ... Alexa T. McCray and William T. Hole ... The process of assigning semantic types to more than 30,000 concepts in the first version of the Metathesaurus (Meta-l), has led to a number of improvements to thepreliminary network described in [3]. These involved, primarily, changes to ...

Annual Symposium on Computer Application in Medical Care, 1995

Abstract Algorithms are described which (1) separated specific medical terms from common English ... more Abstract Algorithms are described which (1) separated specific medical terms from common English words, (2) assigned medical terms to their appropriate specialty (e.g. dermatology, cardiology), and (3) generated and measured the association of pairs of disease attributes in a corpus of structured medical text concerning diseases. The output of these algorithms is discussed in terms of the contributions they may make to the solution of three problems in medical text processing: the construction of knowledge bases about diseases, the querying of such knowledge bases, and the classification of journal articles relevant to diseases.

Annual Symposium on Computer Application in Medical Care, 1993

Most care-giver "knowedge" needs arise at the point of care and are "patient-centered." Many ofts... more Most care-giver "knowedge" needs arise at the point of care and are "patient-centered." Many oftse kowledge needs can be met using existing on-line knowkdge sources, but the process is too time-consuming, currently,for even the computer-profcient. We are developing a set ofpublic domain standards aimed at bringing potentialty relvant knowedge to the point ofcare in a straightforward and timelyfashion. Th stndards will a) make use ofsekcted itemsfrom a Computer-based Patient Record (CPR), e.g., a diagnosis and measure of sevrity, b) anticipate certain care-giver knowkdge needs, e.g., 'therapy," "protocols," "complications," and c) try to satisy those needsfrom availabk bkowkdge sources, e.g., bkowledge-bases, citan datobass, practice guidelines, and on-line t. The standards will use templates, i.e.,f ll-in-the-blan structures, to anticipate knowkdge needs and UMLS@Metahesaurus enhancements to represent the content ofknowkdge sources. Together, the stadrds willform the specV scationfor a "Knowledge-Server" (KS) designed to be accssedfrom any CPR system. Plans are in place to test an interin version ofthis specification in the conte ofmedical oncology. We are accumulating anecdotal evidence that a KS operating in conjunction with a CPR is much more compelling to users than either a CPR or a KS operating alone. Dei a all that mattus: God dwells th, and you neve get to see Him if you don't struagie to get them right-Stphen Jay Gould[l] PDQ Gastrointestinal Cancer Rectal Cancer Cellular Diagnosis Rectal Cancer Adenocarcinoma of the rectum.

Methods of Information in Medicine, 1998

Patient descriptors, or “problems,” such as “brain metastases of melanoma” are an effective way f... more 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 bur...

annual symposium on computer application in medical care, Nov 7, 1990

ABSTRACT The Unified Medical Language System (UMLS) is being developed by the National Library of... more ABSTRACT The Unified Medical Language System (UMLS) is being developed by the National Library of Medicine (NLM) to provide uniform access to computer-based resources in biomedicine. For the foreseeable future, the foundation of the UMLS will be a metathesaurus of biomedical concepts, synthesized from existing biomedical nomenclatures and classification systems. META-1, the first version of the Metathesaurus, is available from the NLM on an experimental basis. It is being distributed on two CD-ROMs, one containing a HyperCard (implementation of META-1, called m-CD™. m-CD is a META-1 browser which will run on a 1MB or larger Apple Macintosh® computer equipped with a CD-ROM reader. Our demonstration of m-CD will assume no special knowledge of Macintoshes or META-1, and it will begin with receipt of META-1 “in the mail”. The demonstration will illustrate ways in which users and developers can use m-CD to explore the contents of META-1.

The last five versions of the Metathesaurus wereproduced using MEMEI, and experience with thatver... more The last five versions of the Metathesaurus wereproduced using MEMEI, and experience with thatversion motivatedthe designofMEMEIH. MEMEIis a concept engine, the first to support a directmanipulation interface. But these manipulationschanged the state ofthe MEMEI database withoutcreatingexternallyinterpretable "actions."A second effort to create an

The National Library of Medicine (NLM) is developing the Unified Medical Language System (UMLS) t... more The National Library of Medicine (NLM) is developing the Unified Medical Language System (UMLS) to provide uniform access to the world's biomedical knowledge. The foundation of the UMLS is a metathesaurus of concept names, or terms. Meta-1, the first version of the Metathesaurus, was synthesized from existing biomedical nomenclatures and classification systems, and it contains in excess of 100,000 terms, including all those from MeSH and DSM, and a portion of those from SNOMED, ICD, CPT, LCSH, COSTAR and other sources. These names are arranged and labeled so as to help answer the questions, “What is it called?” and “Where can I find out more about it?” We refer to the first question as the naming problem, and the second as the location problem, respectively. We think of Meta-1 as a source of lexical diversity and semantic locality with which to address these problems in biomedicine. While the NLM will be using Meta-1 in the UMLS, non-NLM developers and users may wish to use Meta...

The MUMPS programming system was designed and developed to facilitate shared conversational acces... more The MUMPS programming system was designed and developed to facilitate shared conversational access to a hierarchically-organized data base on a small computer. The MUMPS language, which has recently been standardized, contains features for numeric and string operations, along with a built-in file system called globals, embedded in a multiprogrammed execution environment. This paper gives an overview of the MUMPS language and a typical MUMPS system, then evaluates MUMPS in terms of modern notions of programming languages and software development. Despite the many attractive features for the development of interactive programs, MUMPS is seen to have a number of shortcomings when evaluated in this way. Among the problem areas are weakness of control structures, the ability to write self-modifying code, the incomprehensibility of most MUMPS programs, and the lack of support given by the language to notions of abstraction and modularity.

ACM Sigmini Newsletter, Mar 1, 1976

The MUMPS programming system was designed and developed to facilitate shared conversational acces... more The MUMPS programming system was designed and developed to facilitate shared conversational access to a hierarchically-organized data base on a small computer. The MUMPS language, which has recently been standardized, contains features for numeric and string operations, along with a built-in file system called globals, embedded in a multiprogrammed execution environment. This paper gives an overview of the MUMPS language and a typical MUMPS system, then evaluates MUMPS in terms of modern notions of programming languages and software development. Despite the many attractive features for the development of interactive programs, MUMPS is seen to have a number of shortcomings when evaluated in this way. Among the problem areas are weakness of control structures, the ability to write self-modifying code, the incomprehensibility of most MUMPS programs, and the lack of support given by the language to notions of abstraction and modularity.

Proceedings of the Annual Symposium on Computer Application in Medical Care, Nov 7, 1990

... Alexa T. McCray and William T. Hole ... The process of assigning semantic types to more than ... more ... Alexa T. McCray and William T. Hole ... The process of assigning semantic types to more than 30,000 concepts in the first version of the Metathesaurus (Meta-l), has led to a number of improvements to thepreliminary network described in [3]. These involved, primarily, changes to ...

PubMed, 1993

Can new medical knowledge be recognized computationally? We know knowledge is changing, and our k... more 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.

Proceedings of the Annual Symposium on Computer Application in Medical Care, Nov 7, 1990

The UMLS project seeks to provide a unified interface to biomedical knowledge resources. Patient ... more The UMLS project seeks to provide a unified interface to biomedical knowledge resources. Patient medical records are an enormous repository of clinical intervention and outcome, and are drawing increasing attention in the pursuit of quality assurance, outcomes research, and epidemiologic analysis. We sought to evaluate an unedited version of the preliminary UMLS Metathesaurus, Meta-1, for the automated coding of medical diagnosis and surgical procedures. Identical evaluations were undertaken using SNOMED and the Mayo Clinic indexing lexicon. Meta-1 performed comparably to the comparison clinical indexing systems, although all systems exhibited problems associated with clinical attribute levels and modifier combinations.

Proceedings of the Annual Symposium on Computer Application in Medical Care, Nov 7, 1990

One of three knowledge sources being developed as part of the mUm's Ems Project is a bimedical th... more One of three knowledge sources being developed as part of the mUm's Ems Project is a bimedical thesaurus, caled the Metathesaurus. The Metathesaurus contains inter-term relaionshgps across six bomedical nomenclaturs and classfiation systems, deivablefiom lexical mapping techniques. 7he first public version of the Metathesaurus, calledmErA-1, was built In two stages-fuist, source inversion and second, source matching. During the Sprin of 1989, "official" versions for the six sources were obtained In machine-readableform. Source spefic techniques were derived empiicaly to analyze the information structure and content of each source. The results of each analysis wre used to guide the "Inversio of the corresponding source, resulting in a homogeneous representation for all sowrces. The core concepts of META-1 come prmarilyfromMEDuN index terns (MesHO. Previous work on lexical mapping methodology developed algorithmic methods to link cncepts in d(f ferent sources. These methods were refined Iteratively, and used to Iplement a META-1 "!matching engine". The Initial version of META-i was constructed with this engine, by matching the MFrA-1 core concepts to the other sources. This version ofmETA-i was edited and enhanced by domain experts, after the Inclusion of supplemtay informai, to produce thefirst publicly released version ofMErA-1.

Proceedings of the Annual Symposium on Computer Application in Medical Care, Nov 4, 1981

RECONSIDER is an interactive computer program which produces a differential diagnosis given a lis... more RECONSIDER is an interactive computer program which produces a differential diagnosis given a list of patient attributes. The program's principal knowledge base is a corpus of 3,262 disease definitions represented in the form of structured natural language text. As these definitions were originally prepared for human use, RECONSIDER uses medical knowledge that is semantically identical to an information source that might be used by a physician. Thus, RECONSIDER can explain the inclusion of a particular disease in a differential by displaying the way in which the disease's definition relates to the list of patient attributes, and by ranking the strength of this relation relative to the rest of the differential. Use of RECONSIDER is illustrated on cases from the literature, and a case of pyruvate kinase deficiency (PK disease). Included for comparison are cases diagnosed by INTERNIST[1] and PIP[2], two well known diagnosis programs.

Proceedings of the Annual Symposium on Computer Application in Medical Care, Nov 7, 1990

Proceedings of the Annual Symposium on Computer Application in Medical Care, Nov 7, 1990

... Alexa T. McCray and William T. Hole ... The process of assigning semantic types to more than ... more ... Alexa T. McCray and William T. Hole ... The process of assigning semantic types to more than 30,000 concepts in the first version of the Metathesaurus (Meta-l), has led to a number of improvements to thepreliminary network described in [3]. These involved, primarily, changes to ...

Annual Symposium on Computer Application in Medical Care, 1995

Abstract Algorithms are described which (1) separated specific medical terms from common English ... more Abstract Algorithms are described which (1) separated specific medical terms from common English words, (2) assigned medical terms to their appropriate specialty (e.g. dermatology, cardiology), and (3) generated and measured the association of pairs of disease attributes in a corpus of structured medical text concerning diseases. The output of these algorithms is discussed in terms of the contributions they may make to the solution of three problems in medical text processing: the construction of knowledge bases about diseases, the querying of such knowledge bases, and the classification of journal articles relevant to diseases.

Annual Symposium on Computer Application in Medical Care, 1993

Most care-giver "knowedge" needs arise at the point of care and are "patient-centered." Many ofts... more Most care-giver "knowedge" needs arise at the point of care and are "patient-centered." Many oftse kowledge needs can be met using existing on-line knowkdge sources, but the process is too time-consuming, currently,for even the computer-profcient. We are developing a set ofpublic domain standards aimed at bringing potentialty relvant knowedge to the point ofcare in a straightforward and timelyfashion. Th stndards will a) make use ofsekcted itemsfrom a Computer-based Patient Record (CPR), e.g., a diagnosis and measure of sevrity, b) anticipate certain care-giver knowkdge needs, e.g., 'therapy," "protocols," "complications," and c) try to satisy those needsfrom availabk bkowkdge sources, e.g., bkowledge-bases, citan datobass, practice guidelines, and on-line t. The standards will use templates, i.e.,f ll-in-the-blan structures, to anticipate knowkdge needs and UMLS@Metahesaurus enhancements to represent the content ofknowkdge sources. Together, the stadrds willform the specV scationfor a "Knowledge-Server" (KS) designed to be accssedfrom any CPR system. Plans are in place to test an interin version ofthis specification in the conte ofmedical oncology. We are accumulating anecdotal evidence that a KS operating in conjunction with a CPR is much more compelling to users than either a CPR or a KS operating alone. Dei a all that mattus: God dwells th, and you neve get to see Him if you don't struagie to get them right-Stphen Jay Gould[l] PDQ Gastrointestinal Cancer Rectal Cancer Cellular Diagnosis Rectal Cancer Adenocarcinoma of the rectum.

Methods of Information in Medicine, 1998

Patient descriptors, or “problems,” such as “brain metastases of melanoma” are an effective way f... more 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 bur...

annual symposium on computer application in medical care, Nov 7, 1990

ABSTRACT The Unified Medical Language System (UMLS) is being developed by the National Library of... more ABSTRACT The Unified Medical Language System (UMLS) is being developed by the National Library of Medicine (NLM) to provide uniform access to computer-based resources in biomedicine. For the foreseeable future, the foundation of the UMLS will be a metathesaurus of biomedical concepts, synthesized from existing biomedical nomenclatures and classification systems. META-1, the first version of the Metathesaurus, is available from the NLM on an experimental basis. It is being distributed on two CD-ROMs, one containing a HyperCard (implementation of META-1, called m-CD™. m-CD is a META-1 browser which will run on a 1MB or larger Apple Macintosh® computer equipped with a CD-ROM reader. Our demonstration of m-CD will assume no special knowledge of Macintoshes or META-1, and it will begin with receipt of META-1 “in the mail”. The demonstration will illustrate ways in which users and developers can use m-CD to explore the contents of META-1.

The last five versions of the Metathesaurus wereproduced using MEMEI, and experience with thatver... more The last five versions of the Metathesaurus wereproduced using MEMEI, and experience with thatversion motivatedthe designofMEMEIH. MEMEIis a concept engine, the first to support a directmanipulation interface. But these manipulationschanged the state ofthe MEMEI database withoutcreatingexternallyinterpretable "actions."A second effort to create an

The National Library of Medicine (NLM) is developing the Unified Medical Language System (UMLS) t... more The National Library of Medicine (NLM) is developing the Unified Medical Language System (UMLS) to provide uniform access to the world's biomedical knowledge. The foundation of the UMLS is a metathesaurus of concept names, or terms. Meta-1, the first version of the Metathesaurus, was synthesized from existing biomedical nomenclatures and classification systems, and it contains in excess of 100,000 terms, including all those from MeSH and DSM, and a portion of those from SNOMED, ICD, CPT, LCSH, COSTAR and other sources. These names are arranged and labeled so as to help answer the questions, “What is it called?” and “Where can I find out more about it?” We refer to the first question as the naming problem, and the second as the location problem, respectively. We think of Meta-1 as a source of lexical diversity and semantic locality with which to address these problems in biomedicine. While the NLM will be using Meta-1 in the UMLS, non-NLM developers and users may wish to use Meta...