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Items: 17

1.

PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison.

Monnin P, Legrand J, Husson G, Ringot P, Tchechmedjiev A, Jonquet C, Napoli A, Coulet A.

BMC Bioinformatics. 2019 Apr 18;20(Suppl 4):139. doi: 10.1186/s12859-019-2693-9.

2.

Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy.

Venkatesan A, Tagny Ngompe G, Hassouni NE, Chentli I, Guignon V, Jonquet C, Ruiz M, Larmande P.

PLoS One. 2018 Nov 30;13(11):e0198270. doi: 10.1371/journal.pone.0198270. eCollection 2018.

3.

SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes.

Tchechmedjiev A, Abdaoui A, Emonet V, Zevio S, Jonquet C.

BMC Bioinformatics. 2018 Nov 6;19(1):405. doi: 10.1186/s12859-018-2429-2.

4.

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture.

Harper L, Campbell J, Cannon EKS, Jung S, Poelchau M, Walls R, Andorf C, Arnaud E, Berardini TZ, Birkett C, Cannon S, Carson J, Condon B, Cooper L, Dunn N, Elsik CG, Farmer A, Ficklin SP, Grant D, Grau E, Herndon N, Hu ZL, Humann J, Jaiswal P, Jonquet C, Laporte MA, Larmande P, Lazo G, McCarthy F, Menda N, Mungall CJ, Munoz-Torres MC, Naithani S, Nelson R, Nesdill D, Park C, Reecy J, Reiser L, Sanderson LA, Sen TZ, Staton M, Subramaniam S, Tello-Ruiz MK, Unda V, Unni D, Wang L, Ware D, Wegrzyn J, Williams J, Woodhouse M, Yu J, Main D.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay088.

5.

Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator.

Tchechmedjiev A, Abdaoui A, Emonet V, Melzi S, Jonnagaddala J, Jonquet C.

Bioinformatics. 2018 Jun 1;34(11):1962-1965. doi: 10.1093/bioinformatics/bty009.

6.

Developing data interoperability using standards: A wheat community use case.

Dzale Yeumo E, Alaux M, Arnaud E, Aubin S, Baumann U, Buche P, Cooper L, Ćwiek-Kupczyńska H, Davey RP, Fulss RA, Jonquet C, Laporte MA, Larmande P, Pommier C, Protonotarios V, Reverte C, Shrestha R, Subirats I, Venkatesan A, Whan A, Quesneville H.

Version 2. F1000Res. 2017 Oct 16 [revised 2017 Jan 1];6:1843. doi: 10.12688/f1000research.12234.2. eCollection 2017.

7.

NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.

Martínez-Romero M, Jonquet C, O'Connor MJ, Graybeal J, Pazos A, Musen MA.

J Biomed Semantics. 2017 Jun 7;8(1):21. doi: 10.1186/s13326-017-0128-y.

8.

An approach to compare bio-ontologies portals.

Grosjean J, Soualmia LF, Bouarech K, Jonquet C, Darmoni SJ.

Stud Health Technol Inform. 2014;205:1008-12.

PMID:
25160340
9.

NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources.

Jonquet C, Lependu P, Falconer S, Coulet A, Noy NF, Musen MA, Shah NH.

Web Semant. 2011 Sep 1;9(3):316-324.

10.

The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies.

Parai GK, Jonquet C, Xu R, Musen MA, Shah NH.

AMIA Annu Symp Proc. 2010 Nov 13;2010:587-91.

11.

Building a biomedical ontology recommender web service.

Jonquet C, Musen MA, Shah NH.

J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1. doi: 10.1186/2041-1480-1-S1-S1.

12.

A UIMA wrapper for the NCBO annotator.

Roeder C, Jonquet C, Shah NH, Baumgartner WA Jr, Verspoor K, Hunter L.

Bioinformatics. 2010 Jul 15;26(14):1800-1. doi: 10.1093/bioinformatics/btq250. Epub 2010 May 26.

13.

Comparison of concept recognizers for building the Open Biomedical Annotator.

Shah NH, Bhatia N, Jonquet C, Rubin D, Chiang AP, Musen MA.

BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14. doi: 10.1186/1471-2105-10-S9-S14.

14.

BioPortal: ontologies and integrated data resources at the click of a mouse.

Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W170-3. doi: 10.1093/nar/gkp440. Epub 2009 May 29.

15.

Ontology-driven indexing of public datasets for translational bioinformatics.

Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA.

BMC Bioinformatics. 2009 Feb 5;10 Suppl 2:S1. doi: 10.1186/1471-2105-10-S2-S1.

16.

The open biomedical annotator.

Jonquet C, Shah NH, Musen MA.

Summit Transl Bioinform. 2009 Mar 1;2009:56-60.

17.

BioPortal: ontologies and data resources with the click of a mouse.

Musen MA, Shah NH, Noy NF, Dai BY, Dorf M, Griffith N, Buntrok J, Jonquet C, Montegut MJ, Rubin DL.

AMIA Annu Symp Proc. 2008 Nov 6:1223-4. No abstract available.

PMID:
18999306

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