Hematopoietic cell types: prototype for a revised cell ontology.

Journal of Biomedical Informatics
Alexander D DiehlChristopher J Mungall

Abstract

The Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology. The CL is a candidate reference ontology of the OBO Foundry and requires extensive revision to bring it up to current standards for biomedical ontologies, both in its structure and its coverage of various subfields of biology. We have now addressed the specific content of one area of the CL, the section of the ontology dealing with hematopoietic cells. This section has been extensively revised to improve its content and eliminate multiple inheritance in the asserted hierarchy, and the groundwork has been laid for structuring the hematopoietic cell type terms as cross-products incorporating logical definitions built from relationships to external ontologies, such as the Protein Ontology and the Gene Ontology. The methods and improvements to the CL in this area represent a paradigm for improvement of the entire ontology over time.

References

Feb 8, 2005·Genome Biology·Jonathan BardMichael Ashburner
May 17, 2005·Genome Biology·Barry SmithCornelius Rosse
Feb 3, 2007·Bioinformatics·Alexander D DiehlJudith A Blake
Jun 5, 2007·Bioinformatics·John Day-RichterSuzanna Lewis
Dec 6, 2007·BMC Bioinformatics·Darren A NataleCathy H Wu
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Jan 13, 2010·Genome Biology·Christopher J MungallMichael Ashburner
Feb 16, 2010·Journal of Biomedical Informatics·Christopher J MungallJane Lomax

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Citations

Jan 7, 2011·BMC Bioinformatics·Terrence F MeehanAlexander D Diehl
Sep 6, 2013·BMC Bioinformatics·Terrence F MeehanAlexander D Diehl
Jan 5, 2013·Journal of Biomedical Semantics·Mikel Egaña ArangurenMark D Wilkinson
Nov 26, 2013·Nucleic Acids Research·Darren A NataleCathy H Wu
Mar 25, 2011·Methods of Information in Medicine·V MaojoC Kulikowski
Oct 9, 2015·Journal of Biomedical Semantics·Yu LinYongqun He
Jul 15, 2015·Journal of Pathology Informatics·Barry SmithMetin Gurcan
Sep 22, 2015·Journal of Biomedical Semantics·Mikhail K Levin, Lindsay G Cowell
Jan 19, 2011·Journal of Biomedical Informatics·Barry Smith, Richard H Scheuermann
Feb 16, 2010·Journal of Biomedical Informatics·Christopher J MungallJane Lomax
Jul 6, 2016·Journal of Biomedical Semantics·Alexander D DiehlChristopher J Mungall
Apr 25, 2017·Expert Review of Vaccines·Richard H ScheuermannWayne C Koff
Dec 7, 2014·Bioinformatics·Mélanie CourtotRyan R Brinkman
Mar 29, 2018·Human Molecular Genetics·Brian D AevermannRichard H Scheuermann
Jan 13, 2018·BMC Bioinformatics·Trygve BakkenRichard H Scheuermann
Nov 13, 2013·Nucleic Acids Research·Sebastian KöhlerPeter N Robinson
Jul 6, 2019·BMC Bioinformatics·Lucas M SerraAlexander D Diehl
Jul 9, 2020·Bioinformatics·Vasundra TouréMartin Kuiper
Feb 25, 2021·BMC Bioinformatics·Anna Maria MasciUNKNOWN LungMAP Consortium

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