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Items: 1 to 50 of 113

1.

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.

2.

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
3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

PMID:
29016968
8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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
15.

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.

16.

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 VS, 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 TW, 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.

17.

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.

18.

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.

19.

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 VS, 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 TW, Kurreeman F, Allaart CF, Louis Bridges S Jr, Bridges SL, 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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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
28.

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.

29.

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.

30.

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.

31.

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.

32.
33.

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.

34.

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.

35.

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.

36.

An Ebola virus-centered knowledge base.

Kamdar MR, Dumontier M.

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

37.

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.

38.

Toward a complete dataset of drug-drug interaction information from publicly available sources.

Ayvaz S, Horn J, Hassanzadeh O, Zhu Q, Stan J, Tatonetti NP, Vilar S, Brochhausen M, Samwald M, Rastegar-Mojarad M, Dumontier M, Boyce RD.

J Biomed Inform. 2015 Jun;55:206-17. doi: 10.1016/j.jbi.2015.04.006. Epub 2015 Apr 24.

39.

An evidence-based approach to identify aging-related genes in Caenorhabditis elegans.

Callahan A, Cifuentes JJ, Dumontier M.

BMC Bioinformatics. 2015 Feb 7;16:40. doi: 10.1186/s12859-015-0469-4.

40.

Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies.

Samwald M, Miñarro Giménez JA, Boyce RD, Freimuth RR, Adlassnig KP, Dumontier M.

BMC Med Inform Decis Mak. 2015 Feb 22;15:12. doi: 10.1186/s12911-015-0130-1.

41.

Ranking adverse drug reactions with crowdsourcing.

Gottlieb A, Hoehndorf R, Dumontier M, Altman RB.

J Med Internet Res. 2015 Mar 23;17(3):e80. doi: 10.2196/jmir.3962.

42.

Drug-drug interaction data source survey and linking.

Ayvaz S, Zhu Q, Hochheiser H, Brochhausen M, Horn J, Dumontier M, Samwald M, Boyce RD.

AMIA Jt Summits Transl Sci Proc. 2014 Apr 7;2014:16. eCollection 2014.

43.

SPARQL-enabled identifier conversion with Identifiers.org.

Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C.

Bioinformatics. 2015 Jun 1;31(11):1875-7. doi: 10.1093/bioinformatics/btv064. Epub 2015 Jan 31.

44.

Finding our way through phenotypes.

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.

PLoS Biol. 2015 Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection 2015 Jan.

45.

Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest.

Boyce RD, Ryan PB, Norén GN, Schuemie MJ, Reich C, Duke J, Tatonetti NP, Trifirò G, Harpaz R, Overhage JM, Hartzema AG, Khayter M, Voss EA, Lambert CG, Huser V, Dumontier M.

Drug Saf. 2014 Aug;37(8):557-67. doi: 10.1007/s40264-014-0189-0.

46.

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.

Dumontier M, Baker CJ, Baran J, Callahan A, Chepelev L, Cruz-Toledo J, Del Rio NR, Duck G, Furlong LI, Keath N, Klassen D, McCusker JP, Queralt-Rosinach N, Samwald M, Villanueva-Rosales N, Wilkinson MD, Hoehndorf R.

J Biomed Semantics. 2014 Mar 6;5(1):14. doi: 10.1186/2041-1480-5-14.

47.

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T.

J Biomed Semantics. 2014 Feb 5;5(1):5. doi: 10.1186/2041-1480-5-5.

48.

Automatically exposing OpenLifeData via SADI semantic Web Services.

González AR, Callahan A, Cruz-Toledo J, Garcia A, Egaña Aranguren M, Dumontier M, Wilkinson MD.

J Biomed Semantics. 2014 Nov 19;5:46. doi: 10.1186/2041-1480-5-46. eCollection 2014.

49.

Sub-NOAEL amounts of vinclozolin and xenoestrogens target rat chondrogenesis in vivo.

Auxietre TA, Dumontier MF, Balguy I, Frapart Y, Canivenc-Lavier MC, Berges R, Boudalia S, Auger J, Corvol MT, Savouret JF.

Biochimie. 2014 Apr;99:169-77. doi: 10.1016/j.biochi.2013.12.001. Epub 2013 Dec 12.

PMID:
24333988
50.

Mouse model phenotypes provide information about human drug targets.

Hoehndorf R, Hiebert T, Hardy NW, Schofield PN, Gkoutos GV, Dumontier M.

Bioinformatics. 2014 Mar 1;30(5):719-25. doi: 10.1093/bioinformatics/btt613. Epub 2013 Oct 24.

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