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| − | + | ===Curation=== | |
| − | == | + | * [[Guide_to_Character_Annotation | Phenoscape Guide to Character Annotation]] |
| + | ===Anatomy Ontologies=== | ||
| + | * [http://phenoscape.org/wiki/Ontologies#Amniote_Anatomy_Ontology_.28AMAO.29 Amniote Anatomy Ontology (AMAO)] | ||
| + | * [http://phenoscape.org/wiki/Ontologies#Amphibian_Anatomy_Ontology_.28AAO.29 Amphibian Anatomy Ontology (AAO)] | ||
| + | * [http://obofoundry.org/cgi-bin/detail.cgi?caro Common Anatomy Reference Ontology (CARO)] | ||
| + | * [http://phenoscape.org/wiki/Ontologies#Mouse_Adult_Gross_Anatomy_.28MA.29 Mouse Adult Gross Anatomy (MA)] | ||
| + | * [http://phenoscape.org/wiki/Ontologies#Teleost_Anatomy_Ontology_.28TAO.29 Teleost Anatomy Ontology (TAO)] | ||
| + | * [http://obofoundry.org/cgi-bin/detail.cgi?id=uberon Uber Anatomy Ontology (UBERON)] | ||
| + | * [http://phenoscape.org/wiki/Ontologies#Vertebrate_Musculoskeletal_Anatomy_Ontology_.28VAO.29 Vertebrate Skeletal Anatomy Ontology (VSAO)] | ||
| + | * [http://phenoscape.org/wiki/Ontologies#Xenopus_Anatomy_Ontology_.28XAO.29 Xenopus Anatomy Ontology] | ||
| + | * [http://phenoscape.org/wiki/Ontologies#Zebrafish_Anatomical_Ontology_.28ZFA.29 Zebrafish Anatomy and Development (ZFA)] | ||
| + | * [http://obofoundry.org/cgi-bin/detail.cgi?id=quality Phenotype and Trait Ontology (PATO)] | ||
| − | * [http:// | + | ===Anatomy mailing list=== |
| − | ** [http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml | + | Discussion of vertebrate and general anatomy issues are posted to the obo-anatomy list: |
| − | ** [http://www. | + | * 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) | + | * View [http://sourceforge.net/mailarchive/forum.php?forum_name=obo-anatomy obo-anatomy list archives] |
| − | * [http://www.deepfin.org/ DeepFin] | + | |
| + | ===Taxonomy Ontologies=== | ||
| + | * [[Teleost Taxonomy Ontology]] (TTO) | ||
| + | * [[Ontologies#Vertebrate_Taxonomy_Ontology_.28VTO.29| Vertebrate Taxonomy Ontology]] (VTO) | ||
| + | |||
| + | ===Ontology Resources=== | ||
| + | |||
| + | * [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.fruitfly.org/~cjm/obd/formats.html OBD Phenotype file formats] - Includes standards and schemas for PhenoSyntax and PhenoXML | ||
| + | * [http://www.berkeleybop.org/obd/ Open Biomedical Data (OBD) data model, API, and other downloads] | ||
| + | |||
| + | ===Fish resources=== | ||
| + | |||
| + | * [http://www.zfin.org Zebrafish Information Network] (ZFIN) | ||
| + | * [http://www.deepfin.org/ DeepFin] | ||
| + | * [http://silurus.acnatsci.org/ All Catfish Species] | ||
| + | * [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes] | ||
| + | * [http://fishbase.org/ FishBase] | ||
| + | |||
| + | ===Morphology image database resources=== | ||
| + | * [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] | + | * [http://morphobank.geongrid.org/ MorphoBank] |
| − | * [http://digimorph.org/ Digimorph | + | * [http://digimorph.org/ Digimorph] |
| − | |||
| − | |||
| − | |||
* [http://aug.csres.utexas.edu/PhylogenyWiki/ Morphster] | * [http://aug.csres.utexas.edu/PhylogenyWiki/ Morphster] | ||
| − | == | + | ===Software=== |
| + | |||
| + | * [[Phenex]] | ||
| + | * [http://oboedit.org/ OBO-Edit] | ||
| + | *[[ORB term request prototype]] | ||
| + | |||
| + | ===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): | |
| + | * [https://bmir-gforge.stanford.edu/gf/project/bioportal_core/tracker/ BioPortal 2.0 Tracker] at the BMIR GForge installation | ||
| + | * Support email: [mailto:support%40bioontology%2eorg support@bioontology.org] | ||
| − | + | '''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. | |
| − | |||
| − | |||
| − | |||
| − | + | * 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. | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | [[Category:Help]] | |
| − | |||
Latest revision as of 19:39, 24 May 2018
Contents
Curation
Anatomy Ontologies
- Amniote Anatomy Ontology (AMAO)
- Amphibian Anatomy Ontology (AAO)
- Common Anatomy Reference Ontology (CARO)
- Mouse Adult Gross Anatomy (MA)
- Teleost Anatomy Ontology (TAO)
- Uber Anatomy Ontology (UBERON)
- Vertebrate Skeletal Anatomy Ontology (VSAO)
- Xenopus Anatomy Ontology
- Zebrafish Anatomy and Development (ZFA)
- Phenotype and Trait Ontology (PATO)
Anatomy mailing list
Discussion of vertebrate and general anatomy issues are posted to the obo-anatomy list:
- Subscribe or view list archives here: obo-anatomy mailing list
- View obo-anatomy list archives
Taxonomy Ontologies
Ontology Resources
- Ontology browsing and visualization at NCBO
- Maintaining inter-ontology relations between species specific anatomy ontologies and CL/GO/CARO
- OBD Phenotype file formats - Includes standards and schemas for PhenoSyntax and PhenoXML
- Open Biomedical Data (OBD) data model, API, and other downloads
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):
- BioPortal 2.0 Tracker at the BMIR GForge installation
- Support email: support@bioontology.org
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.
- A Basecamp-based BioPortal project management site (login required) has User Group meeting presentations and other information.
