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Items: 1 to 50 of 126

1.

FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources.

Clarke DJB, Wang L, Jones A, Wojciechowicz ML, Torre D, Jagodnik KM, Jenkins SL, McQuilton P, Flamholz Z, Silverstein MC, Schilder BM, Robasky K, Castillo C, Idaszak R, Ahalt SC, Williams J, Schurer S, Cooper DJ, de Miranda Azevedo R, Klenk JA, Haendel MA, Nedzel J, Avillach P, Shimoyama ME, Harris RM, Gamble M, Poten R, Charbonneau AL, Larkin J, Brown CT, Bonazzi VR, Dumontier MJ, Sansone SA, Ma'ayan A.

Cell Syst. 2019 Oct 10. pii: S2405-4712(19)30345-X. doi: 10.1016/j.cels.2019.09.011. [Epub ahead of print]

PMID:
31677972
2.

Author Correction: Evaluating FAIR maturity through a scalable, automated, community-governed framework.

Wilkinson MD, Dumontier M, Sansone SA, Bonino da Silva Santos LO, Prieto M, Batista D, McQuilton P, Kuhn T, Rocca-Serra P, Crosas M, Schultes E.

Sci Data. 2019 Oct 21;6(1):230. doi: 10.1038/s41597-019-0248-6.

3.

Evaluating FAIR maturity through a scalable, automated, community-governed framework.

Wilkinson MD, Dumontier M, Sansone SA, Bonino da Silva Santos LO, Prieto M, Batista D, McQuilton P, Kuhn T, Rocca-Serra P, Crosas M, Schultes E.

Sci Data. 2019 Sep 20;6(1):174. doi: 10.1038/s41597-019-0184-5. Erratum in: Sci Data. 2019 Oct 21;6(1):230.

4.

FAIR Principles for Clinical Practice Guidelines in a Learning Health System.

Leung TI, Dumontier M.

Stud Health Technol Inform. 2019 Aug 21;264:1690-1691. doi: 10.3233/SHTI190599. Review.

PMID:
31438295
5.

A Privacy-Preserving Infrastructure for Analyzing Personal Health Data in a Vertically Partitioned Scenario.

Sun C, Ippel L, van Soest J, Wouters B, Malic A, Adekunle O, van den Berg B, Mussmann O, Koster A, van der Kallen C, van Oppen C, Townend D, Dekker A, Dumontier M.

Stud Health Technol Inform. 2019 Aug 21;264:373-377. doi: 10.3233/SHTI190246.

PMID:
31437948
6.

A Novel Ensemble-Based Machine Learning Algorithm to Predict the Conversion From Mild Cognitive Impairment to Alzheimer's Disease Using Socio-Demographic Characteristics, Clinical Information, and Neuropsychological Measures.

Grassi M, Rouleaux N, Caldirola D, Loewenstein D, Schruers K, Perna G, Dumontier M; Alzheimer's Disease Neuroimaging Initiative.

Front Neurol. 2019 Jul 16;10:756. doi: 10.3389/fneur.2019.00756. eCollection 2019.

7.

Beached microplastics in the Northwestern Mediterranean Sea.

Constant M, Kerhervé P, Mino-Vercellio-Verollet M, Dumontier M, Sànchez Vidal A, Canals M, Heussner S.

Mar Pollut Bull. 2019 May;142:263-273. doi: 10.1016/j.marpolbul.2019.03.032. Epub 2019 Apr 1.

PMID:
31232303
8.

In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data.

Celebi R, Bear Don't Walk O 4th, Movva R, Alpsoy S, Dumontier M.

Sci Rep. 2019 Jun 20;9(1):8949. doi: 10.1038/s41598-019-45236-6.

9.

Putting FAIR Evidence into Practice.

Leung TI, Dumontier M.

J Gen Intern Med. 2019 Aug;34(8):1369. doi: 10.1007/s11606-019-05021-7. No abstract available.

PMID:
31062227
10.

Addendum: The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Jan Aalbersberg I, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, 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, 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 SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Jan Velterop, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B.

Sci Data. 2019 Mar 19;6(1):6. doi: 10.1038/s41597-019-0009-6. No abstract available.

11.

Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records.

Ta CN, Dumontier M, Hripcsak G, Tatonetti NP, Weng C.

Sci Data. 2018 Nov 27;5:180273. doi: 10.1038/sdata.2018.273.

12.

Predicting the need for a reduced drug dose, at first prescription.

Coulet A, Shah NH, Wack M, Chawki MB, Jay N, Dumontier M.

Sci Rep. 2018 Oct 22;8(1):15558. doi: 10.1038/s41598-018-33980-0.

13.

A design framework and exemplar metrics for FAIRness.

Wilkinson MD, Sansone SA, Schultes E, Doorn P, Bonino da Silva Santos LO, Dumontier M.

Sci Data. 2018 Jun 26;5:180118. doi: 10.1038/sdata.2018.118. No abstract available.

14.

Using the Personal Health Train for Automated and Privacy-Preserving Analytics on Vertically Partitioned Data.

van Soest J, Sun C, Mussmann O, Puts M, van den Berg B, Malic A, van Oppen C, Towend D, Dekker A, Dumontier M.

Stud Health Technol Inform. 2018;247:581-585.

PMID:
29678027
15.

Biotea: semantics for Pubmed Central.

Garcia A, Lopez F, Garcia L, Giraldo O, Bucheli V, Dumontier M.

PeerJ. 2018 Jan 2;6:e4201. doi: 10.7717/peerj.4201. eCollection 2018.

16.

BioSearch: a semantic search engine for Bio2RDF.

Hu W, Qiu H, Huang J, Dumontier M.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax059.

17.

Semantics-Powered Healthcare Engineering and Data Analytics.

He Z, Tao C, Bian J, Dumontier M, Hogan WR.

J Healthc Eng. 2017;2017:7983473. doi: 10.1155/2017/7983473. Epub 2017 Oct 26. No abstract available.

18.

Drug-drug interaction extraction via hierarchical RNNs on sequence and shortest dependency paths.

Zhang Y, Zheng W, Lin H, Wang J, Yang Z, Dumontier M.

Bioinformatics. 2018 Mar 1;34(5):828-835. doi: 10.1093/bioinformatics/btx659.

19.

Formalizing drug indications on the road to therapeutic intent.

Nelson SJ, Oprea TI, Ursu O, Bologa CG, Zaveri A, Holmes J, Yang JJ, Mathias SL, Mani S, Tuttle MS, Dumontier M.

J Am Med Inform Assoc. 2017 Nov 1;24(6):1169-1172. doi: 10.1093/jamia/ocx064.

20.

Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata.

Hu W, Zaveri A, Qiu H, Dumontier M.

BMC Bioinformatics. 2017 Sep 18;18(1):415. doi: 10.1186/s12859-017-1832-4.

21.

Discovering associations between adverse drug events using pattern structures and ontologies.

Personeni G, Bresso E, Devignes MD, Dumontier M, Smaïl-Tabbone M, Coulet A.

J Biomed Semantics. 2017 Aug 22;8(1):29. doi: 10.1186/s13326-017-0137-x.

22.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H.

PLoS Biol. 2017 Jun 29;15(6):e2001414. doi: 10.1371/journal.pbio.2001414. eCollection 2017 Jun.

23.

Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO).

Panahiazar M, Dumontier M, Gevaert O.

J Biomed Inform. 2017 Aug;72:132-139. doi: 10.1016/j.jbi.2017.06.017. Epub 2017 Jun 16.

24.

The emergence and evolution of the research fronts in HIV/AIDS research.

Fajardo-Ortiz D, Lopez-Cervantes M, Duran L, Dumontier M, Lara M, Ochoa H, Castano VM.

PLoS One. 2017 May 25;12(5):e0178293. doi: 10.1371/journal.pone.0178293. eCollection 2017.

25.

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop.

Jagodnik KM, Koplev S, Jenkins SL, Ohno-Machado L, Paten B, Schurer SC, Dumontier M, Verborgh R, Bui A, Ping P, McKenna NJ, Madduri R, Pillai A, Ma'ayan A.

J Biomed Inform. 2017 Jul;71:49-57. doi: 10.1016/j.jbi.2017.05.006. Epub 2017 May 10.

26.

Drug-drug interaction discovery and demystification using Semantic Web technologies.

Noor A, Assiri A, Ayvaz S, Clark C, Dumontier M.

J Am Med Inform Assoc. 2017 May 1;24(3):556-564. doi: 10.1093/jamia/ocw128.

PMID:
28031284
27.

Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop.

Verspoor K, Oellrich A, Collier N, Groza T, Rocca-Serra P, Soldatova L, Dumontier M, Shah N.

J Biomed Semantics. 2016 Dec 12;7(1):66.

28.

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium, Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Bridges SL Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM.

Nat Commun. 2016 Oct 10;7:13205. doi: 10.1038/ncomms13205. No abstract available.

29.

The health care and life sciences community profile for dataset descriptions.

Dumontier M, Gray AJG, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall CJ, Rietveld L, Wimalaratne SM, Yamaguchi A.

PeerJ. 2016 Aug 16;4:e2331. doi: 10.7717/peerj.2331. eCollection 2016.

30.

Using LASSO Regression to Predict Rheumatoid Arthritis Treatment Efficacy.

Odgers DJ, Tellis N, Hall H, Dumontier M.

AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:176-83. eCollection 2016.

31.

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium, Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Louis Bridges S Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM.

Nat Commun. 2016 Aug 23;7:12460. doi: 10.1038/ncomms12460. Erratum in: Nat Commun. 2016 Oct 10;7:13205.

32.

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

Bolleman JT, Mungall CJ, Strozzi F, Baran J, Dumontier M, Bonnal RJ, Buels R, Hoehndorf R, Fujisawa T, Katayama T, Cock PJ.

J Biomed Semantics. 2016 Jun 13;7:39. doi: 10.1186/s13326-016-0067-z.

33.

Erratum: Predicting structured metadata from unstructured metadata.

Posch L, Panahiazar M, Dumontier M, Gevaert O.

Database (Oxford). 2016 Jun 13;2016:baw097. doi: 10.1093/database/baw097. eCollection 2016.

34.

Overlap in drug-disease associations between clinical practice guidelines and drug structured product label indications.

Leung TI, Dumontier M.

J Biomed Semantics. 2016 Jun 8;7:37. doi: 10.1186/s13326-016-0081-1.

35.

The Ontology for Biomedical Investigations.

Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ Jr, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J.

PLoS One. 2016 Apr 29;11(4):e0154556. doi: 10.1371/journal.pone.0154556. eCollection 2016.

36.

The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, 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 AJ, Groth P, Goble C, Grethe JS, Heringa J, 't Hoen PA, 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 SA, 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.

Sci Data. 2016 Mar 15;3:160018. doi: 10.1038/sdata.2016.18. Erratum in: Sci Data. 2019 Mar 19;6(1):6.

37.

Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology.

Mortensen JM, Telis N, Hughey JJ, Fan-Minogue H, Van Auken K, Dumontier M, Musen MA.

J Biomed Inform. 2016 Apr;60:199-209. doi: 10.1016/j.jbi.2016.02.005. Epub 2016 Feb 10.

38.

Predicting structured metadata from unstructured metadata.

Posch L, Panahiazar M, Dumontier M, Gevaert O.

Database (Oxford). 2016 Jan 1;2016. doi: 10.1093/database/baw080. Erratum in: Database (Oxford). 2016 Jun 13;2016:baw097.

39.

Special issue on bio-ontologies and phenotypes.

Soldatova LN, Collier N, Oellrich A, Groza T, Verspoor K, Rocca-Serra P, Dumontier M, Shah NH.

J Biomed Semantics. 2015 Dec 17;6:40. doi: 10.1186/s13326-015-0040-2. eCollection 2015.

40.

Analysis of In Vitro Aptamer Selection Parameters.

McKeague M, McConnell EM, Cruz-Toledo J, Bernard ED, Pach A, Mastronardi E, Zhang X, Beking M, Francis T, Giamberardino A, Cabecinha A, Ruscito A, Aranda-Rodriguez R, Dumontier M, DeRosa MC.

J Mol Evol. 2015 Dec;81(5-6):150-61. doi: 10.1007/s00239-015-9708-6. Epub 2015 Nov 3. Review.

PMID:
26530075
41.

Feasibility of Prioritizing Drug-Drug-Event Associations Found in Electronic Health Records.

Banda JM, Callahan A, Winnenburg R, Strasberg HR, Cami A, Reis BY, Vilar S, Hripcsak G, Dumontier M, Shah NH.

Drug Saf. 2016 Jan;39(1):45-57. doi: 10.1007/s40264-015-0352-2.

42.

The digital revolution in phenotyping.

Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M.

Brief Bioinform. 2016 Sep;17(5):819-30. doi: 10.1093/bib/bbv083. Epub 2015 Sep 29.

43.

Automating Identification of Multiple Chronic Conditions in Clinical Practice Guidelines.

Leung TI, Jalal H, Zulman DM, Dumontier M, Owens DK, Musen MA, Goldstein MK.

AMIA Jt Summits Transl Sci Proc. 2015 Mar 25;2015:456-60. eCollection 2015.

44.

Mining Electronic Health Records using Linked Data.

Odgers DJ, Dumontier M.

AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:217-21. eCollection 2015.

45.
46.

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases.

Fu G, Batchelor C, Dumontier M, Hastings J, Willighagen E, Bolton E.

J Cheminform. 2015 Jul 14;7:34. doi: 10.1186/s13321-015-0084-4. eCollection 2015.

47.

Achieving human and machine accessibility of cited data in scholarly publications.

Starr J, Castro E, Crosas M, Dumontier M, Downs RR, Duerr R, Haak LL, Haendel M, Herman I, Hodson S, Hourclé J, Kratz JE, Lin J, Nielsen LH, Nurnberger A, Proell S, Rauber A, Sacchi S, Smith A, Taylor M, Clark T.

PeerJ Comput Sci. 2015;1. pii: e1.

48.

The center for expanded data annotation and retrieval.

Musen MA, Bean CA, Cheung KH, Dumontier M, Durante KA, Gevaert O, Gonzalez-Beltran A, Khatri P, Kleinstein SH, O'Connor MJ, Pouliot Y, Rocca-Serra P, Sansone SA, Wiser JA; CEDAR team.

J Am Med Inform Assoc. 2015 Nov;22(6):1148-52. doi: 10.1093/jamia/ocv048. Epub 2015 Jun 25.

49.

An Ebola virus-centered knowledge base.

Kamdar MR, Dumontier M.

Database (Oxford). 2015 Jun 8;2015:bav049. doi: 10.1093/database/bav049. Print 2015.

50.

GFVO: the Genomic Feature and Variation Ontology.

Baran J, Durgahee BS, Eilbeck K, Antezana E, Hoehndorf R, Dumontier M.

PeerJ. 2015 May 5;3:e933. doi: 10.7717/peerj.933. eCollection 2015.

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