{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T05:08:14Z","timestamp":1770354494196,"version":"3.49.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,27]],"date-time":"2019-08-27T00:00:00Z","timestamp":1566864000000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The South African Research Chairs Initiatives of the Department of Science and Technology and National Research Foundation of South Africa","award":["UID 64751"],"award-info":[{"award-number":["UID 64751"]}]},{"DOI":"10.13039\/501100001322","name":"South African Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001322","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Recent advancements in genomic technologies have enabled high throughput cost-effective generation of \u2018omics\u2019 data from M.tuberculosis (M.tb) isolates, which then gets shared via a number of heterogeneous publicly available biological databases. Albeit useful, fragmented curation negatively impacts the researcher\u2019s ability to leverage the data via federated queries.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present Combat-TB-NeoDB, an integrated M.tb \u2018omics\u2019 knowledge-base. Combat-TB-NeoDB is based on Neo4j and was created by binding the labeled property graph model to a suitable ontology namely Chado. Combat-TB-NeoDB enables researchers to execute complex federated queries by linking prominent biological databases, and supplementary M.tb variants data from published literature.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The Combat-TB-NeoDB (https:\/\/neodb.sanbi.ac.za) repository and all tools mentioned in this manuscript are freely available at https:\/\/github.com\/COMBAT-TB.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz658","type":"journal-article","created":{"date-parts":[[2019,8,22]],"date-time":"2019-08-22T03:21:07Z","timestamp":1566444067000},"page":"982-983","source":"Crossref","is-referenced-by-count":9,"title":["COMBAT-TB-NeoDB: fostering tuberculosis research through integrative analysis using graph database technologies"],"prefix":"10.1093","volume":"36","author":[{"given":"Thoba","family":"Lose","sequence":"first","affiliation":[{"name":"South African National Bioinformatics Institute, South African MRC Bioinformatics Unit, University of the Western Cape , Bellville, 7535, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"van Heusden","sequence":"additional","affiliation":[{"name":"South African National Bioinformatics Institute, South African MRC Bioinformatics Unit, University of the Western Cape , Bellville, 7535, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0420-2916","authenticated-orcid":false,"given":"Alan","family":"Christoffels","sequence":"additional","affiliation":[{"name":"South African National Bioinformatics Institute, South African MRC Bioinformatics Unit, University of the Western Cape , Bellville, 7535, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,8,26]]},"reference":[{"key":"2023013110080226400_btz658-B1","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1093\/bioinformatics\/btw731","article-title":"Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks","volume":"33","author":"Balaur","year":"2017","journal-title":"Bioinformatics"},{"key":"2023013110080226400_btz658-B2","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/s13073-015-0164-0","article-title":"Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences","volume":"7","author":"Coll","year":"2015","journal-title":"Genome Med"},{"key":"2023013110080226400_btz658-B3","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2005-6-5-r44","article-title":"The Sequence Ontology: a tool for the unification of genome annotations","volume":"6","author":"Eilbeck","year":"2005","journal-title":"Genome Biol"},{"key":"2023013110080226400_btz658-B4","doi-asserted-by":"crossref","first-page":"D649","DOI":"10.1093\/nar\/gkx1132","article-title":"The reactome pathway knowledgebase","volume":"46","author":"Fabregat","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023013110080226400_btz658-B5","doi-asserted-by":"crossref","first-page":"1908","DOI":"10.1128\/JCM.00025-15","article-title":"PhyResSE: a web tool delineating Mycobacterium tuberculosis antibiotic resistance and lineage from whole-genome sequencing data","volume":"53","author":"Feuerriegel","year":"2015","journal-title":"J. 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