Difference between revisions of "Links"

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===Curation===
  
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==Links relevant to the project==
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* [[Guide_to_Character_Annotation | Phenoscape Guide to Character Annotation]]
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===Anatomy Ontologies===
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* [http://phenoscape.org/wiki/Ontologies#Amniote_Anatomy_Ontology_.28AMAO.29 Amniote Anatomy Ontology (AMAO)]
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* [http://phenoscape.org/wiki/Ontologies#Amphibian_Anatomy_Ontology_.28AAO.29 Amphibian Anatomy Ontology (AAO)]
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* [http://obofoundry.org/cgi-bin/detail.cgi?caro Common Anatomy Reference Ontology (CARO)]
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* [http://phenoscape.org/wiki/Ontologies#Mouse_Adult_Gross_Anatomy_.28MA.29 Mouse Adult Gross Anatomy (MA)]
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* [http://phenoscape.org/wiki/Ontologies#Teleost_Anatomy_Ontology_.28TAO.29 Teleost Anatomy Ontology (TAO)]
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* [http://obofoundry.org/cgi-bin/detail.cgi?id=uberon Uber Anatomy Ontology (UBERON)]
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* [http://phenoscape.org/wiki/Ontologies#Vertebrate_Musculoskeletal_Anatomy_Ontology_.28VAO.29 Vertebrate Skeletal Anatomy Ontology (VSAO)]
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* [http://phenoscape.org/wiki/Ontologies#Xenopus_Anatomy_Ontology_.28XAO.29 Xenopus Anatomy Ontology]
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* [http://phenoscape.org/wiki/Ontologies#Zebrafish_Anatomical_Ontology_.28ZFA.29 Zebrafish Anatomy and Development (ZFA)]
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* [http://obofoundry.org/cgi-bin/detail.cgi?id=quality Phenotype and Trait Ontology (PATO)]
  
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===Ontologies===
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===Anatomy mailing list===
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Discussion of vertebrate and general anatomy issues are posted to the obo-anatomy list:
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* Subscribe or view list archives here: [http://lists.sourceforge.net/lists/listinfo/obo-anatomy obo-anatomy mailing list]
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* View [http://sourceforge.net/mailarchive/forum.php?forum_name=obo-anatomy obo-anatomy list archives]
  
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'''[http://www.bioontology.org National Center for Biomedical Ontology]'''
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===Taxonomy Ontologies===
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* [http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml Ontologies from NCBO]
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* [[Teleost Taxonomy Ontology]] (TTO)
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* [http://obofoundry.org/cgi-bin/detail.cgi?id=zebrafish_anatomy&title=Zebrafish%20anatomy%20and%20development Ontology of Zebrafish Anatomy and Development]
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* [[Ontologies#Vertebrate_Taxonomy_Ontology_.28VTO.29| Vertebrate Taxonomy Ontology]] (VTO)
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* [http://obofoundry.org/cgi-bin/detail.cgi?caro Common Anatomy Reference Ontology (CARO)] ([http://purl.org/obo/owl/CARO also available in OWL format])
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===Ontology Resources===
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* [http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml Ontology browsing and visualization at NCBO]
 
* [http://www.bioontology.org/wiki/index.php/CL:Aligning_species-specific_anatomy_ontologies_with_CL Maintaining inter-ontology relations between species specific anatomy ontologies and CL/GO/CARO]
 
* [http://www.bioontology.org/wiki/index.php/CL:Aligning_species-specific_anatomy_ontologies_with_CL Maintaining inter-ontology relations between species specific anatomy ontologies and CL/GO/CARO]
 
* [http://www.fruitfly.org/~cjm/obd/formats.html OBD Phenotype file formats] - Includes standards and schemas for PhenoSyntax and PhenoXML
 
* [http://www.fruitfly.org/~cjm/obd/formats.html OBD Phenotype file formats] - Includes standards and schemas for PhenoSyntax and PhenoXML
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* [http://www.berkeleybop.org/obd/ Open Biomedical Data (OBD) data model, API, and other downloads]
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'''Data typed using phenotype ontology'''
 
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* [http://www.phenotypeontology.org/phenotype_annotation/ OBD data and schema downloads]
 
  
 
===Fish resources===
 
===Fish resources===
  
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* [http://www.zfin.org Zebrafish Information Network] (ZFIN)  
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* [http://www.zfin.org Zebrafish Information Network] (ZFIN)
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* [http://www.deepfin.org/ DeepFin]  
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* [http://www.deepfin.org/ DeepFin]
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* [http://www.digitalfishlibrary.org/ Digital Fish Library]
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* [http://silurus.acnatsci.org/ All Catfish Species]
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* [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes]
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* [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes]
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* [http://fishbase.org/ FishBase]  
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* [http://fishbase.org/ FishBase]
  
 
===Morphology image database resources===
 
===Morphology image database resources===
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* [https://www.flickr.com/photos/109282112@N02/ Phenoscape flickr account]
 
* [http://www.morphbank.net/ Morphbank]
 
* [http://www.morphbank.net/ Morphbank]
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* [http://morphobank.geongrid.org/ MorphoBank]
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* [http://morphobank.geongrid.org/ MorphoBank]
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* [http://digimorph.org/ Digimorph]
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* [http://digimorph.org/ Digimorph]
 
* [http://aug.csres.utexas.edu/PhylogenyWiki/ Morphster]
 
* [http://aug.csres.utexas.edu/PhylogenyWiki/ Morphster]
  
 
===Software===
 
===Software===
  
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* [http://www.phenote.org Phenote]
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* [[Phenex]]
 
* [http://oboedit.org/ OBO-Edit]
 
* [http://oboedit.org/ OBO-Edit]
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*[[ORB term request prototype]]
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===NCBO BioPortal support requests===
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Support (for issues) and feature requests for the NCBO BioPortal can be submitted through the following venues (according to Benjamin Dai, BioPortal Lead Software Architect):
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* [https://bmir-gforge.stanford.edu/gf/project/bioportal_core/tracker/ BioPortal 2.0 Tracker] at the BMIR GForge installation
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* Support email: [mailto:support%40bioontology%2eorg support&#64;bioontology&#46;org]
  
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==Bibliography==
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'''NCBO BioPortal User Group:'''
  
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We also maintain a list of references on [http://www.connotea.org Connotea], using the tag "[http://www.connotea.org/tag/phenomap phenomap]". This list may be more up-to-date than the bibliography below.
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We are a (voting) member of the BioPortal User Group. The group has monthly teleconferences where new features are being discusses and subsequently prioritized through survey-voting.
  
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Anyone can easily recommend references (and in fact any site or resource) to us simply by tagging it with "phenomap" in Connotea.
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* A Basecamp-based [https://ncboprojects.updatelog.com/projects/1487611/project/log BioPortal project management site] (login required) has User Group meeting presentations and other information.
  
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===Reprints===
 
  
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* Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. (2008) [[Media:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5.
 
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* Mabee PM et al (2007a). [[Media:TREE Mabee.pdf|Phenotype ontologies: the bridge between genomics and evolution.]] Trends Ecol Evol <cite>mabee2007a</cite>
 
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* Mabee PM et al (2007b). [[Media: JEZ Mabee.pdf|Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish.]] J Exp Zoolog B Mol Dev Evol. <cite>mabee2007b</cite>
 
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* Schulz et al (2007). [http://www.biomedcentral.com/1471-2105/8/134 Spatial location and its relevance for terminological inferences in bio-ontologies.] BMC Bioinformatics 2007, 8:134 [http://dx.doi.org/10.1186/1471-2105-8-134 doi:10.1186/1471-2105-8-134]
 
  
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===References===
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[[Category:Help]]
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<biblio>
 
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#mabee2007a pmid=17416439
 
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#mabee2007b pmid=17599725
 
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#rosen1974 Rosen DE. 1974. ''[http://hdl.handle.net/2246/606 Phylogeny and zoogeography of salmoniform fishes and relationships of Lepidogalaxias salamandroides].'' Bulletin of the American Museum of Natural History 153:267-325.
 
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#finkfink1981 Fink SV, Fink WL. 1981. ''Interrelationships of the ostariophysan fishes (Teleostei)''. Zoological Journal of the Linnean Society 72(4):297-353.
 
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#finkfink1997 Fink, S.V. and W.L. Fink. 1997. Interrelationships of the Ostariophysi. In: ''Interrelationships of Fishes'', M. Stiassney, L. Parenti and D. Johnson (Eds). Academic Press, 209-249.
 
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</biblio>
 

Latest revision as of 19:39, 24 May 2018

Curation

Anatomy Ontologies

Anatomy mailing list

Discussion of vertebrate and general anatomy issues are posted to the obo-anatomy list:

Taxonomy Ontologies

Ontology Resources

Fish resources

Morphology image database resources

Software

NCBO BioPortal support requests

Support (for issues) and feature requests for the NCBO BioPortal can be submitted through the following venues (according to Benjamin Dai, BioPortal Lead Software Architect):

NCBO BioPortal User Group:

We are a (voting) member of the BioPortal User Group. The group has monthly teleconferences where new features are being discusses and subsequently prioritized through survey-voting.

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