phyloref clade-ontology issues

phyloref / clade-ontology

Ontology of Phylogenetic Clade Definitions

MIT License

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Add phyloreferences curated by Rebecca Stubbs over summer 2018

#45 gaurav opened 6 years ago
0
Support the OWL RL profile

#44 gaurav closed 6 years ago
1
Switch to FaCT++ reasoner

#43 gaurav closed 6 years ago
4
Updated Phyloref Ontology IRIs as per phyloref/phyloref-ontology#21

#42 gaurav closed 6 years ago
1
Fixed Phyloref Ontology IRI as per phyloref/phyloref-ontology#21

#41 gaurav closed 6 years ago
1
Add git-crypt-ed folder for storing embargoed phyloreferences

#40 gaurav closed 6 years ago
1
hasInternalSpecifier and hasExternalSpecifier should be removed unless they're needed

#39 gaurav opened 6 years ago
0
Add support for private phyloreferences

#38 gaurav opened 6 years ago
4
Determine licensing for the Clade Ontology

#37 gaurav opened 6 years ago
3
Improve testing of long-running PHYX files

#36 gaurav opened 6 years ago
1
Update README and rename directories in line with new terminology

#35 gaurav closed 6 years ago
4
Create a table of all included phyloreferences

#34 gaurav opened 6 years ago
2
Copy terms we use from other community ontologies into our ontology

#33 gaurav opened 6 years ago
0
Updated Clade Ontology to include and support Wojciechowski, 2003

#32 gaurav closed 6 years ago
1
Allow phyloreferences to indicate whether they are expected to resolve or not

#31 gaurav closed 6 years ago
1
Overhaul README information

#30 hlapp closed 6 years ago
0
Added Brochu 2003 to the ontology of phyloreferences

#29 gaurav closed 6 years ago
2
Identify and write tests for outstanding Unicode encoding issues

#28 gaurav opened 6 years ago
0
Add support for phyloreferences with multiple external specifiers

#27 gaurav opened 6 years ago
1
Add terms for recording curator comments and verbatim specifiers

#26 gaurav closed 6 years ago
1
Move 'paper-context.json' to a permanent fixed location so that all PHYX files can refer to it

#25 gaurav closed 6 years ago
2
Replace "additional labels" with proper taxonomic units

#24 gaurav closed 6 years ago
1
Separate phyx2owl/phyloref into a separate Python library

#23 gaurav opened 6 years ago
0
Look for new formats for storing phylogenies in JSON-LD that are superior to Newick

#22 gaurav opened 6 years ago
0
Rename JSON-LD input files to the PHYX file format

#21 gaurav closed 6 years ago
1
Clean up scratch ontology by removing unused terms

#20 gaurav opened 6 years ago
2
Rename repository from "curation-workflow" to "ontology-of-phyloreferences"

#19 gaurav closed 6 years ago
5
Rename "testcase" to "study"

#18 gaurav opened 6 years ago
0
Basic specimen matching

#17 gaurav closed 6 years ago
3
Confusion between scientific name and dwc:scientificName

#16 gaurav opened 6 years ago
0
Remove requirement for a root @id

#15 gaurav closed 6 years ago
0
Maintaining in-development and stable versions of phyloref_testcase.owl

#14 gaurav opened 6 years ago
1
Design a workflow for formalizing terms in phyloref_testcase.owl

#13 gaurav opened 6 years ago
1
Standardize case and formatting in JSON representation of studies

#12 gaurav closed 6 years ago
1
Detect unmatched specifiers and report to the rest of the testing infrastructure

#11 gaurav closed 6 years ago
1
Added a Python library to faciliate creating the JSON-LD version of the test suite

#10 gaurav closed 6 years ago
1
Add support for detecting specifiers entirely missing from the phylogeny

#9 gaurav closed 6 years ago
1
Add support for specimen mapping

#8 gaurav closed 6 years ago
0
Added a Python library to faciliate creating the JSON-LD version of the test suite

#7 gaurav closed 6 years ago
4
Cleanly separate phyloreferences and specifiers from the matching logic

#6 gaurav closed 6 years ago
0
Clean up add-labels.py so it will be easier to modify and improve

#5 gaurav closed 6 years ago
0
Extract phyloreferences from Crowl and Cellinese 2017

#4 gaurav opened 7 years ago
0
Extract phyloreferences from Tank and Donoghue (2010)

#3 gaurav opened 7 years ago
0
Extract phyloreferences from Cantino et al. 2007

#2 gaurav opened 7 years ago
0
Make phyloreference definitions more ontological and formal

#1 gaurav opened 7 years ago
0