[ { "key": "IDZJ57EW", "version": 2, "library": { "type": "group", "id": 61053, "name": "Bio-ontologies and homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/61053/items/IDZJ57EW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology/items/IDZJ57EW", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/61053/items/I5IX264D", "type": "application/json" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "IDZJ57EW", "version": 2, "parentItem": "I5IX264D", "itemType": "attachment", "linkMode": "imported_file", "title": "Wagner - 1989 - The origin of morphological characters and the bio.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Wagner - 1989 - The origin of morphological characters and the bio.pdf", "md5": "a726a7200d131d7a6eff1b1e61210983", "mtime": 1316166838000, "tags": [], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/UPE49T3W" }, "dateAdded": "2012-02-02T12:49:31Z", "dateModified": "2012-02-02T12:49:31Z" } }, { "key": "I5IX264D", "version": 1, "library": { "type": "group", "id": 61053, "name": "Bio-ontologies and homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/61053/items/I5IX264D", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology/items/I5IX264D", "type": "text/html" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "creatorSummary": "Wagner", "parsedDate": "1989", "numChildren": 1 }, "data": { "key": "I5IX264D", "version": 1, "itemType": "journalArticle", "title": "The origin of morphological characters and the biological basis of homology", "creators": [ { "creatorType": "author", "firstName": "G. P.", "lastName": "Wagner" } ], "abstractNote": "A homolog is a part of the phenotype that is homologous to equivalent parts in other species. A biological homology concept is expected to explain three properties of homologs: 1) the conservation of those features that are used to define a homolog, 2) the individualization of the homolog with regard to the rest of the body, and 3) the uniqueness of homologs, i.e., their specificity for monophyletic groups. The main obstacle to describing a mechanistic basis for homology is the variability of the developmental pathways of undoubtedly homologous characters. However, not all aspects of the developmental pathway are of equal importance. The only organizational features of the developmental system that matter are those that have been historically acquired and cause developmental constraints on the further evolutionary modification of the characters. Two main factors contribute to historically acquired developmental constraints: generative rules of pattern formation and ontogenetic networks. In particular, hierarchical and cyclical inductive networks have the required properties to explain homology. How common such networks are is an open empirical question. The development and variation of pectoral fin hooks in blenniid fishes is presented as a model for the study of a simple ontogenetic network", "publicationTitle": "Evolution", "publisher": "", "place": "", "date": "1989", "volume": "43", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "1157-1171", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "0000", "rights": "", "extra": "", "tags": [], "collections": [ "9JVZMBEG" ], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/28VT6ZTP" }, "dateAdded": "2012-02-02T12:49:31Z", "dateModified": "2012-02-02T12:49:31Z" } }, { "key": "I2GTJFT9", "version": 2, "library": { "type": "group", "id": 61053, "name": "Bio-ontologies and homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/61053/items/I2GTJFT9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology/items/I2GTJFT9", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/61053/items/XE2TK2X6", "type": "application/json" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "I2GTJFT9", "version": 2, "parentItem": "XE2TK2X6", "itemType": "attachment", "linkMode": "imported_file", "title": "Farris - 1967 - The Meaning of Relationship and Taxonomic Procedur.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Farris - 1967 - The Meaning of Relationship and Taxonomic Procedur.pdf", "md5": "a3393237367deac04fa2d93b19b1603c", "mtime": 1326713438936, "tags": [], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/2MUUDZQR" }, "dateAdded": "2012-02-02T12:42:51Z", "dateModified": "2012-02-02T12:42:51Z" } }, { "key": "XE2TK2X6", "version": 1, "library": { "type": "group", "id": 61053, "name": "Bio-ontologies and homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/61053/items/XE2TK2X6", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology/items/XE2TK2X6", "type": "text/html" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "creatorSummary": "Farris", "parsedDate": "1967", "numChildren": 1 }, "data": { "key": "XE2TK2X6", "version": 1, "itemType": "journalArticle", "title": "The Meaning of Relationship and Taxonomic Procedure", "creators": [ { "creatorType": "author", "firstName": "J.S.", "lastName": "Farris" } ], "abstractNote": "The meaning of \"relationship\" in taxonomy is discussed. An exact meaning of evolution- ary relationship is derived, and operational methods for placing organisms according to evolutionary relationship are considered.", "publicationTitle": "Systematic Zoology", "publisher": "", "place": "", "date": "1967", "volume": "16", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "44-51", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Syst. Zool.", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "9JVZMBEG" ], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/PE2ZUBIV" }, "dateAdded": "2012-02-02T12:42:51Z", "dateModified": "2012-02-02T12:42:51Z" } }, { "key": "PJBWPJIW", "version": 2, "library": { "type": "group", "id": 61053, "name": "Bio-ontologies and homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/61053/items/PJBWPJIW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology/items/PJBWPJIW", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/61053/items/UCCGC3NM", "type": "application/json" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "PJBWPJIW", "version": 2, "parentItem": "UCCGC3NM", "itemType": "attachment", "linkMode": "imported_file", "title": "McKitrick - 1994 - On homology and the ontological relationship of pa.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "McKitrick - 1994 - On homology and the ontological relationship of pa.pdf", "md5": "1c52267602a6734009ab4b71d6687594", "mtime": 1322062743395, "tags": [], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/ZW5E7D9F" }, "dateAdded": "2012-02-02T12:42:09Z", "dateModified": "2012-02-02T12:42:09Z" } }, { "key": "UCCGC3NM", "version": 1, "library": { "type": "group", "id": 61053, "name": "Bio-ontologies and homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/61053/items/UCCGC3NM", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology/items/UCCGC3NM", "type": "text/html" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "creatorSummary": "McKitrick", "parsedDate": "1994", "numChildren": 1 }, "data": { "key": "UCCGC3NM", "version": 1, "itemType": "journalArticle", "title": "On homology and the ontological relationship of parts", "creators": [ { "creatorType": "author", "firstName": "M.C.", "lastName": "McKitrick" } ], "abstractNote": "", "publicationTitle": "Systematic Biology", "publisher": "", "place": "", "date": "1994", "volume": "43", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "1", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "9JVZMBEG", "KGWBI58M" ], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/M8PA7T3T" }, "dateAdded": "2012-02-02T12:42:09Z", "dateModified": "2012-02-02T12:42:09Z" } }, { "key": "2FFA2TIB", "version": 2, "library": { "type": "group", "id": 61053, "name": "Bio-ontologies and homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/61053/items/2FFA2TIB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology/items/2FFA2TIB", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/61053/items/RAUJ3S8K", "type": "application/json" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "2FFA2TIB", "version": 2, "parentItem": "RAUJ3S8K", "itemType": "attachment", "linkMode": "imported_file", "title": "Ghiselin - 2005 - Homology as a relation of correspondence between p.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Ghiselin - 2005 - Homology as a relation of correspondence between p.pdf", "md5": "82f86ddd51a18ef820e91064361bc157", "mtime": 1316167012000, "tags": [], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/BKGT32KF" }, "dateAdded": "2012-02-02T12:41:45Z", "dateModified": "2012-02-02T12:41:45Z" } }, { "key": "RAUJ3S8K", "version": 1, "library": { "type": "group", "id": 61053, "name": "Bio-ontologies and homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/61053/items/RAUJ3S8K", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology/items/RAUJ3S8K", "type": "text/html" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "creatorSummary": "Ghiselin", "parsedDate": "2005", "numChildren": 1 }, "data": { "key": "RAUJ3S8K", "version": 1, "itemType": "journalArticle", "title": "Homology as a relation of correspondence between parts of individuals.", "creators": [ { "creatorType": "author", "firstName": "Michael T.", "lastName": "Ghiselin" } ], "abstractNote": "The recognition of correspondences has long been a fundamental activity among\nsystematists. Advocates of Naturphilosophie, such as Lorenz Oken, drew far-fetched analogies\nbetween taxonomic groups and all sorts of other things, including the Persons of the Trinity.\nThey treated change through time either as analogous to an ontogeny or as the product of\ndivinely instituted laws of nature. Darwin changed things by making the taxonomic units\nstrictly historical, implying that they are not classes but rather individuals in a broad\nmetaphysical sense. That means that taxa are concrete, particular things, or wholes made up of\nparts which are themselves individuals, and that there are no laws of nature for them.\nHomology is a relationship of correspondence between parts of organisms that are also parts\nof populations and lineages. It is not a relationship of similarity, and unlike similarity it is\ntransitive. Analogy is a relationship of correspondence between parts of organisms that are\nmembers of classes, and is not necessarily due to function. Taxa, like other individuals, can\nchange indefinitely, and the only thing that they must share is a common ancestor. They do\nnot share an essence, Platonic Idea or Bauplan, although \"conservative characters\" may be\nwidespread in them. Iterative homology likewise is a relationship of correspondence, but the\nnature of that correspondence remains unclear. The difficulties of the homology concept can be overcome by treating phylogenetics and comparative biology in general as historical\nnarrative.", "publicationTitle": "Theory in Biosciences", "publisher": "", "place": "", "date": "2005", "volume": "124", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "91-103", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "0000", "rights": "", "extra": "", "tags": [], "collections": [ "9JVZMBEG", "KGWBI58M" ], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/A8EP49H9" }, "dateAdded": "2012-02-02T12:41:45Z", "dateModified": "2012-02-02T12:41:45Z" } }, { "key": "IWJ29VAJ", "version": 2, "library": { "type": "group", "id": 61053, "name": "Bio-ontologies and homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/61053/items/IWJ29VAJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology/items/IWJ29VAJ", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/61053/items/8BJZIPUU", "type": "application/json" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "IWJ29VAJ", "version": 2, "parentItem": "8BJZIPUU", "itemType": "attachment", "linkMode": "imported_file", "title": "Roux et Robinson-Rechavi - An ontology to clarify homology-related concepts.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Roux et Robinson-Rechavi - An ontology to clarify homology-related concepts.pdf", "md5": "d75074418c1a8394c62eee66845b1dc6", "mtime": 1303394996120, "tags": [], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/AAB2MHT2" }, "dateAdded": "2012-02-02T12:36:27Z", "dateModified": "2012-02-02T12:36:27Z" } }, { "key": "8BJZIPUU", "version": 1, "library": { "type": "group", "id": 61053, "name": "Bio-ontologies and homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/61053/items/8BJZIPUU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology/items/8BJZIPUU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "creatorSummary": "Roux and Robinson-Rechavi", "numChildren": 1 }, "data": { "key": "8BJZIPUU", "version": 1, "itemType": "journalArticle", "title": "An ontology to clarify homology-related concepts", "creators": [ { "creatorType": "author", "firstName": "Julien", "lastName": "Roux" }, { "creatorType": "author", "firstName": "Marc", "lastName": "Robinson-Rechavi" } ], "abstractNote": "", "publicationTitle": "Trends in genetics", "publisher": "", "place": "", "date": "", "volume": "799", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "1-3", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "TIG", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "KGWBI58M" ], "relations": { "owl:sameAs": "http://zotero.org/groups/24910/items/R4WCP7TK" }, "dateAdded": "2012-02-02T12:36:27Z", "dateModified": "2012-02-02T12:36:27Z" } }, { "key": "NXVVTGHX", "version": 2, "library": { "type": "group", "id": 61053, "name": "Bio-ontologies and homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/61053/items/NXVVTGHX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology/items/NXVVTGHX", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/61053/items/6RECUKNN", "type": "application/json" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "NXVVTGHX", "version": 2, "parentItem": "6RECUKNN", "itemType": "attachment", "linkMode": "imported_file", "title": "Parmentier et al. - 2010 - Homolonto generating homology relationships by pa.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Parmentier et al. - 2010 - Homolonto generating homology relationships by pa.pdf", "md5": "88c3daae91dfbbf47c3fedf91c0cd24b", "mtime": 1322063964581, "tags": [], "relations": {}, "dateAdded": "2011-11-23T15:59:16Z", "dateModified": "2011-11-23T15:59:25Z" } }, { "key": "6RECUKNN", "version": 1, "library": { "type": "group", "id": 61053, "name": "Bio-ontologies and homology", "links": { "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/61053/items/6RECUKNN", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bio-ontologies_and_homology/items/6RECUKNN", "type": "text/html" } }, "meta": { "createdByUser": { "id": 132431, "username": "Anais Grand", "name": "Grand Anais", "links": { "alternate": { "href": "https://www.zotero.org/anais_grand", "type": "text/html" } } }, "creatorSummary": "Parmentier et al.", "parsedDate": "2010", "numChildren": 1 }, "data": { "key": "6RECUKNN", "version": 1, "itemType": "journalArticle", "title": "Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy", "creators": [ { "creatorType": "author", "firstName": "G.", "lastName": "Parmentier" }, { "creatorType": "author", "firstName": "F.B.", "lastName": "Bastian" }, { "creatorType": "author", "firstName": "M.", "lastName": "Robinson-Rechavi" } ], "abstractNote": "", "publicationTitle": "Bioinformatics", "publisher": "", "place": "", "date": "2010", "volume": "26", "issue": "14", "section": "", "partNumber": "", "partTitle": "", "pages": "1766–1771", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Homolonto", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "KGWBI58M" ], "relations": {}, "dateAdded": "2011-11-23T15:59:20Z", "dateModified": "2011-11-23T15:59:20Z" } } ]