Cook DL - Search Results

1

Harmonizing semantic annotations for computational models in biology.

Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D. Neal ML, et al. Among authors: cook dl. Brief Bioinform. 2019 Mar 22;20(2):540-550. doi: 10.1093/bib/bby087. Brief Bioinform. 2019. PMID: 30462164 Free PMC article. Review.

2

Integration of multi-scale biosimulation models via light-weight semantics.

Gennari JH, Neal ML, Carlson BE, Cook DL. Gennari JH, et al. Among authors: cook dl. Pac Symp Biocomput. 2008:414-25. Pac Symp Biocomput. 2008. PMID: 18229704 Free PMC article.

3

Advances in semantic representation for multiscale biosimulation: a case study in merging models.

Neal ML, Gennari JH, Arts T, Cook DL. Neal ML, et al. Among authors: cook dl. Pac Symp Biocomput. 2009:304-15. Pac Symp Biocomput. 2009. PMID: 19209710 Free PMC article.

4

Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies.

Cook DL, Mejino JL, Neal ML, Gennari JH. Cook DL, et al. Annu Int Conf IEEE Eng Med Biol Soc. 2009;2009:2791-4. doi: 10.1109/IEMBS.2009.5333830. Annu Int Conf IEEE Eng Med Biol Soc. 2009. PMID: 19964601 Free PMC article.

5

SemGen: a tool for semantics-based annotation and composition of biosimulation models.

Neal ML, Thompson CT, Kim KG, James RC, Cook DL, Carlson BE, Gennari JH. Neal ML, et al. Among authors: cook dl. Bioinformatics. 2019 May 1;35(9):1600-1602. doi: 10.1093/bioinformatics/bty829. Bioinformatics. 2019. PMID: 30256901 Free PMC article.

6

Multiple ontologies in action: composite annotations for biosimulation models.

Gennari JH, Neal ML, Galdzicki M, Cook DL. Gennari JH, et al. Among authors: cook dl. J Biomed Inform. 2011 Feb;44(1):146-54. doi: 10.1016/j.jbi.2010.06.007. Epub 2010 Jun 30. J Biomed Inform. 2011. PMID: 20601121 Free PMC article.

7

Bridging biological ontologies and biosimulation: the ontology of physics for biology.

Cook DL, Mejino JL, Neal ML, Gennari JH. Cook DL, et al. AMIA Annu Symp Proc. 2008 Nov 6;2008:136-40. AMIA Annu Symp Proc. 2008. PMID: 18999003 Free PMC article.

8

Integrating systems biology models and biomedical ontologies.

Hoehndorf R, Dumontier M, Gennari JH, Wimalaratne S, de Bono B, Cook DL, Gkoutos GV. Hoehndorf R, et al. Among authors: cook dl. BMC Syst Biol. 2011 Aug 11;5:124. doi: 10.1186/1752-0509-5-124. BMC Syst Biol. 2011. PMID: 21835028 Free PMC article.

9

Physical properties of biological entities: an introduction to the ontology of physics for biology.

Cook DL, Bookstein FL, Gennari JH. Cook DL, et al. PLoS One. 2011;6(12):e28708. doi: 10.1371/journal.pone.0028708. Epub 2011 Dec 27. PLoS One. 2011. PMID: 22216106 Free PMC article.

10

Ontology of physics for biology: representing physical dependencies as a basis for biological processes.

Cook DL, Neal ML, Bookstein FL, Gennari JH. Cook DL, et al. J Biomed Semantics. 2013 Dec 2;4(1):41. doi: 10.1186/2041-1480-4-41. J Biomed Semantics. 2013. PMID: 24295137 Free PMC article.

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