On the CL ontology maintained by Diehl (or precursor to it?)
\ngrumble: the Background section assumes I know what a cell type is:
\n\n\nthe annotation of these phenotypes is hampered by a lack of structured information describing a variety of other biological objects, including cell types
\n
But the next para has what I need, i.e. example queries:
\n\n\nIts use will allow a biologist to query a single database with such questions as: list all of the cell types in mouse that express the Notch gene and all of the cell types in Drosophila and Caenorhabditis elegans that express the closest homolog of this gene; list all of the genes in mouse, rat, human and zebrafish that are expressed in the cell type Schwann_cell; CL:0000218; list all of the genes in D. melanogaster and C. elegans that have a mutant phenotype in the cell types that develop from the cell type myoblast; CL:0000056.
\n
Umm...
\n\n\nThis approach does, however, pose conceptual problems: for example, are a mammalian 'muscle_cell' and a nematode 'muscle_cell' homologous?
\n
Time to go to wikipedia school on Homology (biology)
\n\n\nIn evolutionary biology, homology refers to any similarity between characteristics of organisms that is due to their shared ancestry. ... Anatomical structures that perform the same function in different biological species and evolved from the same structure in some ancestor species are homologous.
\nThe concept of homology is contrasted with that of analogy, which refers to two structures that perform the same or similar function by a similar mechanism but evolved separately.
\nHomology among proteins and DNA is often concluded on the basis of sequence similarity, especially in bioinformatics.
\n
So the question about muscle cells is a question of fact, not of ontology design. I'm puzzled. Ah... OK... the rest of the para clarifies.
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molecules 2005: human cell differentiation molecules", "creators": [ { "creatorType": "author", "firstName": "Heddy", "lastName": "Zola" }, { "creatorType": "author", "firstName": "Bernadette", "lastName": "Swart" }, { "creatorType": "author", "firstName": "Ian", "lastName": "Nicholson" }, { "creatorType": "author", "firstName": "Bent", "lastName": "Aasted" }, { "creatorType": "author", "firstName": "Armand", "lastName": "Bensussan" }, { "creatorType": "author", "firstName": "Laurence", "lastName": "Boumsell" }, { "creatorType": "author", "firstName": "Chris", "lastName": "Buckley" }, { "creatorType": "author", "firstName": "Georgina", "lastName": "Clark" }, { "creatorType": "author", "firstName": "Karel", "lastName": "Drbal" }, { "creatorType": "author", "firstName": "Pablo", "lastName": "Engel" }, { "creatorType": "author", "firstName": "Derek", "lastName": "Hart" }, { "creatorType": "author", "firstName": "Vaclav", "lastName": "Horejsi" }, { "creatorType": "author", "firstName": 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matrices, with infectious agents, and with other antigens. 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"text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/15278/items/D59BX987", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cell_markers_and_flow_cytometry/items/D59BX987", "type": "text/html" } }, "meta": { "createdByUser": { "id": 201035, "username": "connolly", "name": "Dan Connolly", "links": { "alternate": { "href": "https://www.zotero.org/connolly", "type": "text/html" } } }, "creatorSummary": "Voss", "parsedDate": "2007", "numChildren": 2 }, "data": { "key": "D59BX987", "version": 1, "itemType": "bookSection", "title": "Leukocyte Membrane Molecules—An Introduction", "creators": [ { "creatorType": "author", "firstName": "E.", "lastName": "Voss" } ], "abstractNote": "", "bookTitle": "", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "2007", "publisher": "Wiley", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "pages": "", "ISBN": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2010-04-05T16:17:39Z", "dateModified": "2010-04-05T16:17:39Z" } }, { "key": "4A3JCV9N", "version": 3080, "library": { "type": "group", "id": 15278, "name": "Cell markers and flow cytometry", "links": { "alternate": { "href": "https://www.zotero.org/groups/cell_markers_and_flow_cytometry", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/15278/items/4A3JCV9N", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cell_markers_and_flow_cytometry/items/4A3JCV9N", "type": "text/html" } }, "meta": { "createdByUser": { "id": 201035, "username": "connolly", "name": "Dan Connolly", "links": { "alternate": { "href": "https://www.zotero.org/connolly", "type": "text/html" } } }, "creatorSummary": "Masci et al.", "parsedDate": "2009", "numChildren": 1 }, "data": { "key": "4A3JCV9N", "version": 3080, "itemType": "journalArticle", "title": "An improved ontological representation of dendritic cells as a paradigm for all cell types", "creators": [ { "creatorType": "author", "firstName": "Anna Maria", "lastName": "Masci" }, { "creatorType": "author", "firstName": "Cecilia N", "lastName": "Arighi" }, { "creatorType": "author", "firstName": "Alexander D", "lastName": "Diehl" }, { "creatorType": "author", "firstName": "Anne E", "lastName": "Lieberman" }, { "creatorType": "author", "firstName": "Chris", "lastName": "Mungall" }, { "creatorType": "author", "firstName": "Richard H", "lastName": "Scheuermann" }, { "creatorType": "author", "firstName": "Barry", "lastName": "Smith" }, { "creatorType": "author", "firstName": "Lindsay G", "lastName": "Cowell" } ], "abstractNote": "BACKGROUND: Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure and formal rigor of ontologies to better support computation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL's utility for computation and for cross-species data integration. RESULTS: To enhance the CL's utility for computational analyses, we developed a method for the ontological representation of cells and applied this method to develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. We avoid multiple uses of is_a by linking DC-CL terms to terms in other ontologies via additional, formally defined relations such as has_function. CONCLUSION: This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. Accordingly, we propose our method as a general strategy for the ontological representation of cells. DC-CL is available from http://www.obofoundry.org.", "publicationTitle": "BMC Bioinformatics", "publisher": "", "place": "", "date": "2009", "volume": "10", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "70", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "BMC Bioinformatics", "DOI": "10.1186/1471-2105-10-70", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/19243617", "accessDate": "2010-04-02T23:01:45Z", "PMID": "19243617", "PMCID": "", "ISSN": "1471-2105", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Computational Biology", "type": 1 }, { "tag": "Databases, Factual", "type": 1 }, { "tag": "Dendritic Cells", "type": 1 }, { "tag": "Information Storage and Retrieval", "type": 1 }, { "tag": "Terminology as Topic", "type": 1 }, { "tag": "Vocabulary, Controlled", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2010-04-05T16:17:20Z", "dateModified": "2010-04-05T16:17:20Z" } }, { "key": "CTIDDF2X", "version": 1, "library": { "type": "group", "id": 15278, "name": "Cell markers and flow cytometry", "links": { "alternate": { "href": "https://www.zotero.org/groups/cell_markers_and_flow_cytometry", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/15278/items/CTIDDF2X", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/cell_markers_and_flow_cytometry/items/CTIDDF2X", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/15278/items/EPESZMJ8", "type": "application/json" } }, "meta": { "createdByUser": { "id": 201035, "username": "connolly", "name": "Dan Connolly", "links": { "alternate": { "href": "https://www.zotero.org/connolly", "type": "text/html" } } } }, "data": { "key": "CTIDDF2X", "version": 1, "parentItem": "EPESZMJ8", "itemType": "attachment", "linkMode": "linked_url", "title": "Amazon.com Link", "accessDate": "2010-04-02T20:57:29Z", "url": "http://www.amazon.com/dp/0471701327", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2010-04-05T16:17:20Z", "dateModified": "2010-04-05T16:17:20Z" } } ]In evolutionary biology, homology refers to any similarity between characteristics of organisms that is due to their shared ancestry. ... Anatomical structures that perform the same function in different biological species and evolved from the same structure in some ancestor species are homologous.
\nThe concept of homology is contrasted with that of analogy, which refers to two structures that perform the same or similar function by a similar mechanism but evolved separately.
\nHomology among proteins and DNA is often concluded on the basis of sequence similarity, especially in bioinformatics.
\n