Difference between revisions of "Links"

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(Links relevant to the project)
(Anatomy Ontologies)
 
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===Curation===
  
==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)]
  
* [http://www.bioontology.org National Center for Biomedical Ontology]
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===Anatomy mailing list===
** [http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml Ontologies from NCBO]
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Discussion of vertebrate and general anatomy issues are posted to the obo-anatomy list:
** [http://www.phenote.org Phenote]  
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* Subscribe or view list archives here: [http://lists.sourceforge.net/lists/listinfo/obo-anatomy obo-anatomy mailing list]
* [http://www.zfin.org Zebrafish Information Network] (ZFIN)  
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* View [http://sourceforge.net/mailarchive/forum.php?forum_name=obo-anatomy obo-anatomy list archives]
* [http://www.deepfin.org/ DeepFin]  
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===Taxonomy Ontologies===
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* [[Teleost Taxonomy Ontology]] (TTO)
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* [[Ontologies#Vertebrate_Taxonomy_Ontology_.28VTO.29| Vertebrate Taxonomy Ontology]] (VTO)
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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]
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* [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]
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* [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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===Fish resources===
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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://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://fishbase.org/ FishBase]
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===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]
* [http://morphobank.geongrid.org/ MorphoBank]
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* [http://morphobank.geongrid.org/ MorphoBank]
* [http://digimorph.org/ Digimorph
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* [http://digimorph.org/ Digimorph]
* [http://www.digitalfishlibrary.org/ Digital Fish Library] 
 
* [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes] 
 
* [http://fishbase.org/ FishBase]  
 
 
* [http://aug.csres.utexas.edu/PhylogenyWiki/ Morphster]
 
* [http://aug.csres.utexas.edu/PhylogenyWiki/ Morphster]
  
==Bibliography==
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===Software===
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* [[Phenex]]
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* [http://oboedit.org/ OBO-Edit]
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*[[ORB term request prototype]]
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===NCBO BioPortal support requests===
  
===Reprints===
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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]
  
* Mabee PM et al (2007). [[Media:TREE Mabee.pdf|Phenotype ontologies: the bridge between genomics and evolution.]] Trends Ecol Evol <cite>mabee2007</cite>
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'''NCBO BioPortal User Group:'''
* 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]
 
  
===References===
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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.
<biblio>
 
#mabee2007 pmid=17416439
 
</biblio>
 
  
==Local Links==
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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.
  
; Hotel
 
* [http://www.millenniumhotels.com/MCIL.nsf/LU_HOTELDOC/113$$HotelDescription?OpenDocument Millenium Hotel]
 
  
; Dining & Entertainment
 
* [http://www.ninthst.com/ Ninth Street] (right across from NESCent)
 
  
; Historic
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[[Category:Help]]
* [http://www.owdna.org/mill.htm Erwin Mills]
 

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.