Gonçalves RS, O’Connor MJ, Martínez-Romero M, Graybeal J, Musen MA: Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies. arXiv [cs.DB] 2017.
Wilkinson MD, Dumontier M, Aalbersberg IJJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten J-W, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, ’ t Hoen PAC, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone S-A, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B: The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 2016, 3:160018.
Article
PubMed
PubMed Central
Google Scholar
Shadbolt N, Berners-Lee T, Hall W. The semantic web revisited. IEEE Intell Syst. 2006;21:96–101.
Article
Google Scholar
Whetzel PL, NCBO Team. NCBO Technology: Powering semantically aware applications. J Biomed Semantics. 2013;4(Suppl 1):S8.
Article
PubMed
PubMed Central
Google Scholar
Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics. 2013;29:1325–32.
Article
PubMed
PubMed Central
CAS
Google Scholar
ZOOMA text annotations tool. http://www.ebi.ac.uk/spot/zooma/.
Jonquet C, Shah NH, Youn CH, Callendar C, Storey M-A, Musen MA. NCBO annotator: semantic annotation of biomedical data. International Semantic Web Conference, Poster and Demo session. 2009. https://pdfs.semanticscholar.org/9956/898d4012bb87374931085a643eb06b18ac9f.pdf.
Martínez-Romero M, Jonquet C, O’Connor MJ, Graybeal J, Pazos A, Musen MA. NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. J Biomed Semantics. 2017;8:21.
Article
PubMed
PubMed Central
Google Scholar
Brazma A. Minimum information about a microarray experiment (MIAME)--successes, failures, challenges. Sci World J. 2009;9:420–3.
Article
CAS
Google Scholar
Rubelt F, Busse CE, Bukhari SAC, Bürckert J-P, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc M-P, Scott JK, Breden F. AIRR community, Luning Prak ET, Kleinstein SH: adaptive immune receptor repertoire community recommendations for sharing immune-repertoire sequencing data. Nat Immunol. 2017;18:1274–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse C, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen F, Wine Y, Laserson U, Klatzmann D, Douek D, Lefranc M-P, Collins AM, Bubela T, Kleinstein S, Watson CT, Cowell LG, Scott JK, Kepler TB. Perspective: Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol. 2017;8.
Kettner C, Field D, Sansone S-A, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL. Meeting report from the second “minimum information for biological and biomedical investigations” (MIBBI) workshop. Stand Genomic Sci. 2010;3:259–66.
Article
PubMed
PubMed Central
Google Scholar
Musen MA, Bean CA, Cheung K-H, Dumontier M, Durante KA, Gevaert O, Gonzalez-Beltran A, Khatri P, Kleinstein SH, O’Connor MJ, Pouliot Y, Rocca-Serra P, Sansone S-A, Wiser JA. CEDAR team: the center for expanded data annotation and retrieval. J Am Med Inform Assoc. 2015;22:1148–52.
PubMed
PubMed Central
Google Scholar
Bukhari SAC, O'Connor MJ, Graybeal J, Musen MA, Cheung K-H, Kleinstein SH. Leveraging the CEDAR Workbench for Ontology-linked Submission of Adaptive Immune Receptor Repertoire Data to the Sequence Read Archive (SRA). https://doi.org/10.6084/m9.figshare.4244126.v3.
Mehta P. Introduction to Google Chrome Extensions. In: Creating Google Chrome Extensions: Apress. New Delhi: Spinger; 2016. p. 1–33. https://link.springer.com/content/pdf/10.1007/978-1-4842-1775-7.pdf.
Shital P. Web browser security: different attacks detection and prevention techniques. IJCAI. 2017;170:35–41.
Article
Google Scholar
Wood L, Nicol G, Robie J, Champion M, Byrne S. Document object model (DOM) level 3 core specification. MIT, INRIA, KEO: W3C; 2000.
Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 2008;36:D344–50.
Article
PubMed
CAS
Google Scholar
Schriml LM, Arze C, Nadendla S, Chang Y-WW, Mazaitis M, Felix V, Feng G, Kibbe WA. Disease ontology: a backbone for disease semantic integration. Nucleic Acids Res. 2012;40:D940–6.
Article
PubMed
CAS
Google Scholar
Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R. Gene ontology consortium: the gene ontology (GO) database and informatics resource. Nucleic Acids Res. 2004;32:D258–61.
Article
PubMed
CAS
Google Scholar
Bjoern P and OBI consortium. Ontology for Biomedical Investigations. Available from Nature Precedings; 2009.
Quality Control in Phenotypic Analysis by Flow Cytometry. In: Robinson JP, Darzynkiewicz Z, Dobrucki J, Hyun WC, Nolan JP, Orfao A, Rabinovitch PS, editors. Current Protocols in Cytometry. Hoboken: Wiley; 2001. p. 26:13.
Natale DA, Arighi CN, Barker WC, Blake J, Chang T-C, Hu Z, Liu H, Smith B, Wu CH. Framework for a protein ontology. BMC Bioinformatics. 2007;8(Suppl 9):S1.
Article
PubMed
PubMed Central
CAS
Google Scholar
Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Consortium OBI, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone S-A, Scheuermann RH, Shah N, Whetzel PL, Lewis S. The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007;25:1251–5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Paulson LD. Building rich web applications with Ajax. Computer. 2005;38(10):14-7.
Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey M-A, Chute CG, Musen MA. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009;37:W170–3.
Article
PubMed
PubMed Central
CAS
Google Scholar
Barrett T, Clark K, Gevorgyan R, Gorelenkov V, Gribov E, Karsch-Mizrachi I, Kimelman M, Pruitt KD, Resenchuk S, Tatusova T, Yaschenko E, Ostell J. BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res. 2012;40:D57–63.
Article
PubMed
CAS
Google Scholar
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD. Logical development of the cell ontology. BMC Bioinformatics. 2011;12:6.
Article
PubMed
PubMed Central
Google Scholar
Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. CLO: the cell line ontology. J Biomed Semantics. 2014;5:37.
Article
PubMed
PubMed Central
Google Scholar
Kumar A, Smith B. Oncology ontology in the NCI thesaurus. In: Artificial Intelligence in Medicine. Berlin, Heidelberg: Springer; 2005. p. 213–20.
Chapter
Google Scholar
Federhen S. The NCBI taxonomy database. Nucleic Acids Res. 2012;40:D136–43.
Article
PubMed
CAS
Google Scholar
Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA. Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012;13:R5.
Article
PubMed
PubMed Central
Google Scholar
Sarntivijai S, Xiang Z, Meehan TF, Diehl AD, Vempati U, Schürer SC, Pang C, Malone J, Parkinson HE, Athey BD. Others: cell line ontology: redesigning the cell line knowledgebase to aid integrative translational informatics. ICBO. 2011;833:25–32.
Google Scholar
Kamath C. Scientific data mining: a practical perspective. SIAM; 2009. https://epubs.siam.org/doi/book/10.1137/1.9780898717693.
Tandareanu N, Ghindeanu M. Properties of derivations in a semantic Schema. Annals of the University of Craiova-Mathematics and Computer Science Series. 2006;33:147–53.
Google Scholar
Hartmann J, Palma R, Gómez-Pérez A. Ontology repositories. In: Handbook on Ontologies. Berlin, Heidelberg: Springer; 2009. p. 551–71.
Chapter
Google Scholar
Vita R, Overton JA, Greenbaum JA, Sette A, Peters B. Query enhancement through the practical application of ontology: the IEDB and OBI. J Biomed Semantics. 2013;4(Suppl 1):S6.
Article
PubMed
PubMed Central
Google Scholar
Bukhari SAC, Krauthammer M, Baker CJO. SEBI: an architecture for biomedical image discovery, interoperability and reusability based on semantic enrichment. In: SWAT4LS: Citeseer. Berlin: 7th International Workshop on Semantic Web Applications and Tools for life sciences; 2014.
Bukhari SAC. Semantic enrichment and similarity approximation for biomedical sequence images. Canada: University of New Brunswick (Canada) and ProQuest Dissertations Publishing; 2017.
Lipscomb CE. Medical subject headings (MeSH). Bull Med Libr Assoc. 2000;88:265–6.
PubMed
PubMed Central
CAS
Google Scholar
Kim S, Yeganova L, Wilbur WJ. Meshable: searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms. Bioinformatics. 2016;32:3044–6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Beissinger TM, Morota G. Medical subject heading (MeSH) annotations illuminate maize genetics and evolution. Plant Methods. 2017;13:8.
Article
PubMed
PubMed Central
Google Scholar