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1 parent ec267ba commit de715360041a753a39f40b72280039ac50107912 @cmungall cmungall committed
41 README-editors.txt
@@ -5,7 +5,7 @@ Contributing editors see README-contributing-editors.txt
= Editors file =
-The editors file is currently uberon_edit.obo.
+The editors file is currently uberon_edit.obo
@@ -14,6 +14,7 @@ Workflow:
make uberon-qc
git commit -m 'type message here'
git push
+ # check Jenkins
@@ -25,7 +26,10 @@ Releases:
For now the workflow is to hand edit the file in emacs with obo-mode
on, using a variety of scripts and tools. ordering of stanzas in the
-obo file is optimized for hand-edits. This isn't scalable.
+obo file is optimized for hand-edits.
+Releases need not be made after every edit. Eventually releases will
+be daily and automated via Jenkins.a
= Changes to workflow =
@@ -49,6 +53,9 @@ Moving everything to googlecode may be a good idea, need to check if
larger quotas are possible (we need to manage large OWL files for
+Note: currently googlecode sucks for web viewing of diffs of obo (let
+alone owl). SF is actually much better here.
We could simply move everything to sf svn, but sf has less features
and many don't work well.
@@ -58,10 +65,10 @@ Currently releases are made by typing "make uberon-qc". See the
Makefile for the actual dependencies. This unleashes a massive
pipeline, which involves
- - using the OE reasoner to pre-reason
+ - Using OWLTools and Oort to pre-reason and check for unsats
- using a bevy of perl scripts to check for hand-edit derived errors
- performing a number of semantic verification steps using prolog
- - taxon checks
+ - taxon checks (<--- now done with Elk)
- disjoint violations, spatial disjointness checks
- making derived files
- merged (now done in owltools)
@@ -71,7 +78,8 @@ pipeline, which involves
After which the editor must perform a complicate release process to sf.
This will be changed such as the majority of the release process can
-be carried out by Oort. This will use the majority of Oort's features:
+be carried out by Oort under Jenkins. This will use the majority of
+Oort's features:
- merge in external ontologies
- expand macros, in particular:
@@ -89,8 +97,6 @@ There are a few things needing worked out in Oort:
- selective expansion of macros
- ensure mireoting of relations has correct behavior
- bridge files
-- trick to allow checking for disjoints in Elk
- (hermit doesn't work well with uberon)
== Separation into OWL modules ==
@@ -98,6 +104,8 @@ Rather than having all information in one monolithic obo file we will
progressively place certain subsets of information into owl files that
can be imported using importer ontologies. These will be edited in P4.
+NOTE: this has already been done for phenoscape-ext.owl
Eventually the core will switch to OWL and be edited in P4.
* depiction ontology
@@ -135,27 +143,12 @@ Blocked on:
* ID support in P4 (showstopper?)
* Do full testing of functional syntax
-Good to have:
-* OntoVCS support
-* deterministic order of elements in functional syntax
+* Informative diffs (OntoVCS support?)
+* deterministic order of elements in functional syntax (diffs)
The editors version will most likely owl-import other ontologies. Need
to figure this into release process.
-== Train additional editors ==
-Once the switch to OWL for uberon_edit is made we can increase the
-number of people with edit priveleges, subdivide to taxonomic
-groups. Each should have adequate training. Aim to have this ready for
-summer 2012 workshop.
-We can do further modularization here. E.g. we can make submoules for
-certain domains (e.g. neuroanatomy) or taxa.
-Need to thoroughly test with Oort if we go with mixed IDs
== Other matters ==
How does this work with CL? Synchronize this? Mutual imports?
@@ -0,0 +1,15 @@
+Uberon is a multi-species anatomy ontology.
+If you are reading this, you're probably in the uberon developers
+repository. Unless you're an Uberon developer, you probably want to be
+over on ([].
+This repository contains the editors version of the ontology
+(uberon_edit.obo), and the material required to make a release.
+See the file README-editors.txt
0  cell-to-uberon-via-FMA.txt → experimental/cell-to-uberon-via-FMA.txt
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0  cell-to-uberon-via-ZFA.txt → experimental/cell-to-uberon-via-ZFA.txt
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0  fma_xp_cell.obo → experimental/fma_xp_cell.obo
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0  fma_xp_uberon.obo → experimental/fma_xp_uberon.obo
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0  hog_xp_uberon.obo → experimental/hog_xp_uberon.obo
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0  mouse_anatomy_xp_uberon.obo → experimental/mouse_anatomy_xp_uberon.obo
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0  uberon_CL.obo → experimental/uberon_CL.obo
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0  zebrafish_anatomy_xp_uberon.obo → experimental/zebrafish_anatomy_xp_uberon.obo
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0  mappings-FMA-FBbt-201009.rdf → ext-mappings/mappings-FMA-FBbt-201009.rdf
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0  mappings-FMA-FBbt.rdf → ext-mappings/mappings-FMA-FBbt.rdf
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0  mappings-FMA-MA-201009.rdf → ext-mappings/mappings-FMA-MA-201009.rdf
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0  mappings-FMA-MA.rdf → ext-mappings/mappings-FMA-MA.rdf
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0  mappings-GAZ-FMA.rdf → ext-mappings/mappings-GAZ-FMA.rdf
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0  mappings-ZFA-MA-201009.rdf → ext-mappings/mappings-ZFA-MA-201009.rdf
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0  mappings-ZFA-MA.rdf → ext-mappings/mappings-ZFA-MA.rdf
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0  insect_glossary.obo → resources/insect_glossary.obo
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4,653 uberon-thumbnail-xrefs.obo
0 additions, 4,653 deletions not shown
16 uberon_class_taxon-count.txt
@@ -1,16 +0,0 @@
-NCBITaxon:33213-Bilateria 3995
-NCBITaxon:33316-Coelomata 3991
-NCBITaxon:117571-Euteleostomi 3939
-NCBITaxon:32523-Tetrapoda 3896
-NCBITaxon:314146-Euarchontoglires 3816
-NCBITaxon:9606-Homo sapiens 3400
-NCBITaxon:10088-Mus 2721
-NCBITaxon:32443-Teleostei 911
-NCBITaxon:7955-Danio rerio 907
-NCBITaxon:8292-Amphibia 711
-NCBITaxon:8353-Xenopus 605
-NCBITaxon:6656-Arthropoda 271
-NCBITaxon:33392-Endopterygota 271
-NCBITaxon:7227-Drosophila melanogaster 243
-NCBITaxon:7399-Hymenoptera 161
-NCBITaxon:6239-Caenorhabditis elegans 114
29,952 uberon_class_taxon.txt
0 additions, 29,952 deletions not shown
13 uberon_class_taxon_min-count.txt
@@ -1,13 +0,0 @@
-NCBITaxon:314146-Euarchontoglires 1457
-NCBITaxon:9606-Homo sapiens 991
-NCBITaxon:117571-Euteleostomi 677
-NCBITaxon:10088-Mus 391
-NCBITaxon:33316-Coelomata 132
-NCBITaxon:32523-Tetrapoda 129
-NCBITaxon:33213-Bilateria 110
-NCBITaxon:7955-Danio rerio 32
-NCBITaxon:33392-Endopterygota 25
-NCBITaxon:7227-Drosophila melanogaster 24
-NCBITaxon:8353-Xenopus 16
-NCBITaxon:32443-Teleostei 7
-NCBITaxon:6239-Caenorhabditis elegans 4
3,995 uberon_class_taxon_min.txt
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0  → util/
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