{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:06Z","timestamp":1772138046710,"version":"3.50.1"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2021,6,12]],"date-time":"2021-06-12T00:00:00Z","timestamp":1623456000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institute of Health","doi-asserted-by":"publisher","award":["R01GM104436"],"award-info":[{"award-number":["R01GM104436"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DGE-1632976"],"award-info":[{"award-number":["DGE-1632976"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Experimental findings on genetic disease mechanisms are scattered throughout the literature and represented in many ways, including unstructured text, cartoons, pathway diagrams and network graphs. Integration and structuring of such mechanistic information greatly enhances its utility.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>MecCog is a graphical framework for building integrated representations (mechanism schemas) of mechanisms by which a genetic variant causes a disease phenotype. A MecCog mechanism schema displays the propagation of system perturbations across stages of biological organization, using graphical notations to symbolize perturbed entities and activities, hyperlinked evidence tagging, a mechanism ontology and depiction of knowledge gaps, ambiguities and uncertainties. The web platform enables a user to construct, store, publish, browse, query and comment on schemas. MecCog facilitates the identification of potential biomarkers, therapeutic intervention sites and critical future experiments.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The MecCog framework is freely available at http:\/\/www.meccog.org.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab432","type":"journal-article","created":{"date-parts":[[2021,6,11]],"date-time":"2021-06-11T07:37:34Z","timestamp":1623397054000},"page":"4180-4186","source":"Crossref","is-referenced-by-count":4,"title":["MecCog: a knowledge representation framework for genetic disease mechanism"],"prefix":"10.1093","volume":"37","author":[{"given":"Kunal","family":"Kundu","sequence":"first","affiliation":[{"name":"Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland , College Park, MD 20742,","place":["USA"]},{"name":"Institute for Bioscience and Biotechnology Research, University of Maryland , Rockville, MD 20850,","place":["USA"]}]},{"given":"Lindley","family":"Darden","sequence":"additional","affiliation":[{"name":"Department of Philosophy, University of Maryland , College Park, MD 20742,","place":["USA"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3012-2282","authenticated-orcid":false,"given":"John","family":"Moult","sequence":"additional","affiliation":[{"name":"Institute for Bioscience and Biotechnology Research, University of Maryland , Rockville, MD 20850,","place":["USA"]},{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland , College Park, MD 20742,","place":["USA"]}]}],"member":"286","published-online":{"date-parts":[[2021,6,12]]},"reference":[{"key":"2025052320022487900_btab432-B1","doi-asserted-by":"crossref","first-page":"W530","DOI":"10.1093\/nar\/gky355","article-title":"LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC","volume":"46","author":"Allot","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2025052320022487900_btab432-B2","doi-asserted-by":"crossref","first-page":"2127","DOI":"10.1093\/bioinformatics\/btr339","article-title":"The biological connection markup language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways","volume":"27","author":"Beltrame","year":"2011","journal-title":"Bioinformatics"},{"key":"2025052320022487900_btab432-B3","doi-asserted-by":"crossref","first-page":"D1005","DOI":"10.1093\/nar\/gky1120","article-title":"The NHGRI-EBI GWAS catalog of published genome-wide association studies, targeted arrays and summary statistics 2019","volume":"47","author":"Buniello","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025052320022487900_btab432-B4","doi-asserted-by":"crossref","first-page":"424","DOI":"10.3389\/fgene.2020.00424","article-title":"From GWAS to function: using functional genomics to identify the mechanisms underlying complex diseases","volume":"11","author":"Cano-Gamez","year":"2020","journal-title":"Front. 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