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Comprehensive anatomic ontologies for lung development: A comparison of alveolar formation and maturation within mouse and human lung.

Pan H, Deutsch GH, Wert SE; Ontology Subcommittee; NHLBI Molecular Atlas of Lung Development Program Consortium.

J Biomed Semantics. 2019 Oct 24;10(1):18. doi: 10.1186/s13326-019-0209-1.


LungMAP: The Molecular Atlas of Lung Development Program.

Ardini-Poleske ME, Clark RF, Ansong C, Carson JP, Corley RA, Deutsch GH, Hagood JS, Kaminski N, Mariani TJ, Potter SS, Pryhuber GS, Warburton D, Whitsett JA, Palmer SM, Ambalavanan N; LungMAP Consortium.

Am J Physiol Lung Cell Mol Physiol. 2017 Nov 1;313(5):L733-L740. doi: 10.1152/ajplung.00139.2017. Epub 2017 Aug 10. Review.


Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data.

Hayamizu TF, Baldock RA, Ringwald M.

Mamm Genome. 2015 Oct;26(9-10):422-30. doi: 10.1007/s00335-015-9584-9. Epub 2015 Jul 25.


Integrating partonomic hierarchies in anatomy ontologies.

Burger A, Davidson D, Yang Y, Baldock R.

BMC Bioinformatics. 2004 Nov 26;5:184.


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.


The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species.

Park CA, Bello SM, Smith CL, Hu ZL, Munzenmaier DH, Nigam R, Smith JR, Shimoyama M, Eppig JT, Reecy JM.

J Biomed Semantics. 2013 Aug 9;4(1):13. doi: 10.1186/2041-1480-4-13.


An open annotation ontology for science on web 3.0.

Ciccarese P, Ocana M, Garcia Castro LJ, Das S, Clark T.

J Biomed Semantics. 2011 May 17;2 Suppl 2:S4. doi: 10.1186/2041-1480-2-S2-S4.


Modifier Ontologies for frequency, certainty, degree, and coverage phenotype modifier.

Endara L, Thessen AE, Cole HA, Walls R, Gkoutos G, Cao Y, Chong SS, Cui H.

Biodivers Data J. 2018 Nov 28;(6):e29232. doi: 10.3897/BDJ.6.e29232. eCollection 2018.


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.


BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. doi: 10.1093/nar/gkr469. Epub 2011 Jun 14.


Providing visualisation support for the analysis of anatomy ontology data.

Dadzie AS, Burger A.

BMC Bioinformatics. 2005 Mar 24;6:74.


Owlready: Ontology-oriented programming in Python with automatic classification and high level constructs for biomedical ontologies.

Lamy JB.

Artif Intell Med. 2017 Jul;80:11-28. doi: 10.1016/j.artmed.2017.07.002. Epub 2017 Aug 14.


The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S.

Nat Biotechnol. 2007 Nov;25(11):1251-5.


A common layer of interoperability for biomedical ontologies based on OWL EL.

Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV.

Bioinformatics. 2011 Apr 1;27(7):1001-8. doi: 10.1093/bioinformatics/btr058. Epub 2011 Feb 21.


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.


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.


NCBO Technology: Powering semantically aware applications.

Whetzel PL; NCBO Team.

J Biomed Semantics. 2013 Apr 15;4 Suppl 1:S8. doi: 10.1186/2041-1480-4-S1-S8. Epub 2013 Apr 15.


Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.

Jupp S, Stevens R, Hoehndorf R.

J Biomed Semantics. 2012 Apr 24;3 Suppl 1:S3. doi: 10.1186/2041-1480-3-S1-S3.


Mapping between the OBO and OWL ontology languages.

Tirmizi SH, Aitken S, Moreira DA, Mungall C, Sequeda J, Shah NH, Miranker DP.

J Biomed Semantics. 2011 Mar 7;2 Suppl 1:S3. doi: 10.1186/2041-1480-2-S1-S3.


Building integrated ontological knowledge structures with efficient approximation algorithms.

Xiang Y, Janga SC.

Biomed Res Int. 2015;2015:501528. doi: 10.1155/2015/501528. Epub 2015 Oct 13.

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