Machine aided indexing from natural language text

The NASA Lexical Dictionary (NLD) Machine Aided Indexing (MAI) system was designed to (1) reuse the indexing of the Defense Technical Information Center (DTIC); (2) reuse the indexing of the Department of Energy (DOE); and (3) reduce the time required for original indexing. This was done by automatically generating appropriate NASA thesaurus terms from either the other agency's index terms, or, for original indexing, from document titles and abstracts. The NASA STI Program staff devised two different ways to generate thesaurus terms from text. The first group of programs identified noun phrases by a parsing method that allowed for conjunctions and certain prepositions, on the assumption that indexable concepts are found in such phrases. Results were not always satisfactory, and it was noted that indexable concepts often occurred outside of noun phrases. The first method also proved to be too slow for the ultimate goal of interactive (online) MAI. The second group of programs used the knowledge base (KB), word proximity, and frequency of word and phrase occurrence to identify indexable concepts. Both methods are described and illustrated. Online MAI has been achieved, as well as several spinoff benefits, which are also described

Machine-aided indexing at NASA

This report describes the NASA Lexical Dictionary (NLD), a machine-aided indexing system used online at the National Aeronautics and Space Administration's Center for AeroSpace Information (CASI). This system automatically suggests a set of candidate terms from NASA's controlled vocabulary for any designated natural language text input. The system is comprised of a text processor that is based on the computational, nonsyntactic analysis of input text and an extensive knowledge base that serves to recognize and translate text-extracted concepts. The functions of the various NLD system components are described in detail, and production and quality benefits resulting from the implementation of machine-aided indexing at CASI are discussed

NASA's online machine aided indexing system

This report describes the NASA Lexical Dictionary, a machine aided indexing system used online at the National Aeronautics and Space Administration's Center for Aerospace Information (CASI). This system is comprised of a text processor that is based on the computational, non-syntactic analysis of input text, and an extensive 'knowledge base' that serves to recognize and translate text-extracted concepts. The structure and function of the various NLD system components are described in detail. Methods used for the development of the knowledge base are discussed. Particular attention is given to a statistically-based text analysis program that provides the knowledge base developer with a list of concept-specific phrases extracted from large textual corpora. Production and quality benefits resulting from the integration of machine aided indexing at CASI are discussed along with a number of secondary applications of NLD-derived systems including on-line spell checking and machine aided lexicography

Knowledge-based Machine Indexing From Natural Language Text: Knowledge Base Design, Development, and Maintenance

One strategy for machine-aided indexing (MAI) is to provide a concept-level analysis of the textual elements of documents or document abstracts. In such systems natural-language phrases are analyzed in order to identify and classify concepts related to a particular subject domain. The overall performance of these MAI systems is largely dependent on the quality and comprehensiveness of their knowledge bases. These knowledge bases function to (1) define the relations between a controlled indexing vocabulary and natural language expressions; (2) provide a slmplo mechanism for disambiguation and the determination of relevancy; and (3) allow the exten sion of a concept-hlerarchical structure to all elements of the file. After a brief descriptlon of the NASA Machlne-AJded Indexing system, concerns related to the development and maintenance of MAI knowledge bases are discussed. Particular emphasls Is glven to statistically-based text analysis tools deslgned to ald the knowledge base developer. One such tool, the Knowledge Base Building (KBB) program, presents the domaln expert with a well-filtered list of synonyms and conceptually-related phrases for each thesaurus concept. Another tool, the Knowledge Base Maintenance (KBM) program, functions to identify areas of the knowledge base affected by changes In the conceptual domain, for example, the addition of a new thesaurus term. Analternate use of the KBM as an aid in thesaurus construction Is also discussed

Contribution of mRNA Splicing to Mismatch Repair Gene Sequence Variant Interpretation

Functional assays that assess mRNA splicing can be used in interpretation of the clinical significance of sequence variants, including the Lynch syndrome-associated mismatch repair (MMR) genes. The purpose of this study was to investigate the contribution of splicing assay data to the classification of MMR gene sequence variants. We assayed mRNA splicing for 24 sequence variants in MLH1, MSH2, and MSH6, including 12 missense variants that were also assessed using a cell-free in vitro MMR activity (CIMRA) assay. Multifactorial likelihood analysis was conducted for each variant, combining CIMRA outputs and clinical data where available. We collated these results with existing public data to provide a dataset of splicing assay results for a total of 671 MMR gene sequence variants (328 missense/in-frame indel), and published and unpublished repair activity measurements for 154 of these variants. There were 241 variants for which a splicing aberration was detected: 92 complete impact, 33 incomplete impact, and 116 where it was not possible to determine complete versus incomplete splicing impact. Splicing results mostly aided in the interpretation of intronic (72%) and silent (92%) variants and were the least useful for missense substitutions/in-frame indels (10%). MMR protein functional activity assays were more useful in the analysis of these exonic variants but by design they were not able to detect clinically important splicing aberrations identified by parallel mRNA assays. The development of high throughput assays that can quantitatively assess impact on mRNA transcript expression and protein function in parallel will streamline classification of MMR gene sequence variants. Keywords: Lynch syndrome; mRNA splicing; mismatch repair genes; splicing aberrations; variant interpretation and classification; variant type

Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database

The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome–associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases

Application of a 5-tiered scheme for standardized classification of 2,360 Unique mismatch repair gene variants in the InSiGHT locus-specific database

The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases

Application of a 5-tiered scheme for standardized classification of 2,360 Unique mismatch repair gene variants in the InSiGHT locus-specific database

The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases

Application of a 5-tiered scheme for standardized classification of 2,360 Unique mismatch repair gene variants in the InSiGHT locus-specific database

The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases

Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database.

The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases