Difference between revisions of "Annotator tutorial topics"

From phenoscape
Jump to: navigation, search
(Created page with "Agenda- topics and software for curator training: Overview of curation workflow (see Sandrine’s slides) and software involved ====Ontology development:==== Review of limb term...")
 
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:
 
Agenda- topics and software for curator training:
 
Agenda- topics and software for curator training:
Overview of curation workflow (see Sandrine’s slides) and software involved
+
Overview of curation workflow and software involved
  
 
====Ontology development:====
 
====Ontology development:====
Review of limb terms for Amniote Anatomy Ontology (AMAO) and ontology update
+
Protege tutorial
Amniote Taxonomy (with Peter Midford) and ontology update
+
  
 
====Ontology development principles:====
 
====Ontology development principles:====
OBO foundry principles (orthogonality, single inheritance, versioning, etc...)
+
OBO foundry principles (orthogonality, single inheritance, versioning, etc...)
OBO format (terms, synonyms, identifiers, dbxrefs...)
+
Genus-differentia definitions
Genus-differentia definitions (see [1])
+
Logical relationships
+
  
 
====Online resources and mailing lists (bookmark)====
 
====Online resources and mailing lists (bookmark)====
Term trackers (VAO, VTO, PATO, CARO, Uberon)  
+
Term trackers (PATO, RO, CARO, Uberon)
 +
 
 
OBO Foundry
 
OBO Foundry
 +
 
BioPortal
 
BioPortal
Mailing lists: Phenoscape-curators, Obo-edit Working Group, obo-anatomy, obo-discuss
+
 
 +
Mailing lists: Phenoscape-curators, obo-anatomy, obo-discuss
  
 
====Curation training====
 
====Curation training====
EQ annotation - Review wiki Guide to Character Annotation  
+
EQ annotation - Review wiki Guide to Character Annotation
 +
 
 
Phenex
 
Phenex
 +
 
Matrix and free text entry in Mesquite and/OR direct import into Phenex
 
Matrix and free text entry in Mesquite and/OR direct import into Phenex
SVN and ZigVersion
+
 
 +
Subversion and use of SmartSVN
 +
 
 
Mendeley
 
Mendeley
 +
 
Phenoscape Curation Log in Google Docs
 
Phenoscape Curation Log in Google Docs
 +
 
Taxon lists update
 
Taxon lists update
 +
 
Endnote and publication identifiers
 
Endnote and publication identifiers
  
 
====Ontology editing and updating====
 
====Ontology editing and updating====
OBO-edit
+
SVN, SmartSVN
CVS, SmartCVS; SVN, ZigVersion
+
 
 
Term request workflow; proposed ORB workflow
 
Term request workflow; proposed ORB workflow
Running the reasoner in Obo-Edit
 
Protégé overview?
 
Synchronization Tool
 

Latest revision as of 20:34, 29 November 2012

Agenda- topics and software for curator training: Overview of curation workflow and software involved

Ontology development:

Protege tutorial

Ontology development principles:

OBO foundry principles (orthogonality, single inheritance, versioning, etc...) Genus-differentia definitions

Online resources and mailing lists (bookmark)

Term trackers (PATO, RO, CARO, Uberon)

OBO Foundry

BioPortal

Mailing lists: Phenoscape-curators, obo-anatomy, obo-discuss

Curation training

EQ annotation - Review wiki Guide to Character Annotation

Phenex

Matrix and free text entry in Mesquite and/OR direct import into Phenex

Subversion and use of SmartSVN

Mendeley

Phenoscape Curation Log in Google Docs

Taxon lists update

Endnote and publication identifiers

Ontology editing and updating

SVN, SmartSVN

Term request workflow; proposed ORB workflow