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kltm / dupes.txt
Created July 19, 2022 23:39
Dupes during GO-CAM loading
2022-07-19 15:49:08,650 ERROR (org.geneontology.minerva.cli.CommandLineInterface:470) Attempted to load gocam ttl file into database but gocam with that iri already exists, skipping /home/bbop/local/src/git/noctua-models/models/DETOX1-PWY-DETOX1-PWY.ttl http://model.geneontology.org/DETOX1-PWY
2022-07-19 15:50:59,703 ERROR (org.geneontology.minerva.cli.CommandLineInterface:470) Attempted to load gocam ttl file into database but gocam with that iri already exists, skipping /home/bbop/local/src/git/noctua-models/models/PWY-821-1.ttl http://model.geneontology.org/PWY-821-1
2022-07-19 15:51:59,757 ERROR (org.geneontology.minerva.cli.CommandLineInterface:470) Attempted to load gocam ttl file into database but gocam with that iri already exists, skipping /home/bbop/local/src/git/noctua-models/models/P4-PWY-1-P4-PWY-1.ttl http://model.geneontology.org/P4-PWY-1
2022-07-19 15:52:34,584 ERROR (org.geneontology.minerva.cli.CommandLineInterface:470) Attempted to load gocam ttl file into database but gocam with that iri a
@kltm
kltm / goa_human_complex-report.html
Created February 15, 2022 21:02
2022-02-15 snapshot goa_human_complex-report.html
This file has been truncated, but you can view the full file.
Table of contents
Report (original)
Predictions (original)
Predictions (experimental) (original)
Report
Group: goa - Dataset: goa_human_complex
SUMMARY
@kltm
kltm / chebi_rhea_reactome.diff
Created January 31, 2022 22:25
diff output for chebi in rhea vs chebi in reactome
> CHEBI:18356
> CHEBI:18357
3817a2609,2610
> CHEBI:18360
> CHEBI:18362
3820a2614,2615
> CHEBI:18367
> CHEBI:18368
3821a2617,2622
> CHEBI:18371
@kltm
kltm / sparql.txt
Created November 18, 2021 20:38
Big SPARQL query that makes kittens cry
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX pr: <http://purl.org/ontology/prv/core#>
PREFIX metago: <http://model.geneontology.org/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX obo: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX providedBy: <http://purl.org/pav/providedBy>
PREFIX MF: <http://purl.obolibrary.org/obo/GO_0003674>
PREFIX causally_upstream_of_or_within: <http://purl.obolibrary.org/obo/RO_0002418>
@kltm
kltm / traceback.txt
Created November 12, 2021 18:04
python3 ontobio/io/differ.py --file1 /tmp/noctua_mgi-src.gpad --file2 /tmp/noctua_mgi-src.gpad --output /tmp/test.b.out --group_by_column DB_Object_ID --group_by_column Evidence_type
(env) sjcarbon@moiraine:~/local/src/git/ontobio[gpad_differ]$:( python3 ontobio/io/differ.py --file1 /tmp/noctua_mgi-src.gpad --file2 /tmp/noctua_mgi-src.gpad --output /tmp/test.b.out --group_by_column DB_Object_ID --group_by_column Evidence_type
/home/sjcarbon/local/src/git/ontobio/env/lib/python3.7/site-packages/rdflib_jsonld/__init__.py:12: DeprecationWarning: The rdflib-jsonld package has been integrated into rdflib as of rdflib==6.0.1. Please remove rdflib-jsonld from your project's dependencies.
DeprecationWarning,
Traceback (most recent call last):
File "ontobio/io/differ.py", line 354, in <module>
compare_files()
File "/home/sjcarbon/local/src/git/ontobio/env/lib/python3.7/site-packages/click/core.py", line 1128, in __call__
return self.main(*args, **kwargs)
File "/home/sjcarbon/local/src/git/ontobio/env/lib/python3.7/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
@kltm
kltm / release-log.2021-10-25
Created October 26, 2021 16:11
17:12:06 /usr/local/lib/python3.6/dist-packages/rdflib_jsonld/__init__.py:12: DeprecationWarning: The rdflib-jsonld package has been integrated into rdflib as of rdflib==6.0.1. Please remove rdflib-jsonld from your project's dependencies.
17:12:06 DeprecationWarning,
17:12:07 /usr/local/lib/python3.6/dist-packages/rdflib_jsonld/__init__.py:12: DeprecationWarning: The rdflib-jsonld package has been integrated into rdflib as of rdflib==6.0.1. Please remove rdflib-jsonld from your project's dependencies.
17:12:07 DeprecationWarning,
17:12:07 Traceback (most recent call last):
17:12:07 File "/usr/local/bin/validate.py", line 32, in <module>
17:12:07 from ontobio.rdfgen.gocamgen.gocam_builder import GoCamBuilder, AssocExtractor
17:12:07 File "/usr/local/lib/python3.6/dist-packages/ontobio/rdfgen/gocamgen/gocam_builder.py", line 1, in <module>
17:12:07 from ontobio.rdfgen.gocamgen.gocamgen import AssocGoCamModel
17:12:07 File "/usr/local/lib/python3.6/dist-packages/ontobio/rdfgen/gocam
@kltm
kltm / all_obo_issues.txt
Created September 16, 2021 03:19
All OBOFoundry issues
COB 185
COB 184
COB 182
COB 181
COB 176
COB 174
COB 169
COB 168
COB 163
COB 161
@kltm
kltm / all.log
Created September 16, 2021 02:29
All committers to OBOFoundry
25 Author: abessiari <aessiari@lbl.gov>
2 Author: adrien-barton <adrien-barton@users.noreply.github.com>
3 Author: aellenhicks <aellenhicks@gmail.com>
18 Author: alanruttenberg <alanruttenberg@gmail.com>
54 Author: Alan Ruttenberg <alanruttenberg@gmail.com>
7 Author: Alejandra Gonzalez-Beltran <alejandra.gonzalez.beltran@gmail.com>
2 Author: Allyson Lister <allyson.lister@oerc.ox.ac.uk>
5 Author: Andrew Su <andrew.su@gmail.com>
38 Author: Apurva Mody <28663318+apmody@users.noreply.github.com>
3 Author: Asiyah Yu Lin <linikujp@gmail.com>
@kltm
kltm / neo-sgd.obo, ids-only
Created August 25, 2021 23:19
IDs from NEO OBO file for SGD
id: SGD:S000002429
id: SGD:S000028797
id: SGD:S000000878
id: SGD:S000001420
id: SGD:S000003566
id: SGD:S000000138
id: SGD:S000000021
id: SGD:S000000499
id: SGD:S000000500
id: SGD:S000000139
@kltm
kltm / untracked.txt
Created July 21, 2021 19:05
GO-CAMs on noctua-dec that are untracked
models/-1022290586.ttl
models/6074794600000000.ttl
models/6074794600000004.ttl
models/ACETATEUTIL2-PWY.ttl
models/AERO-GLYCEROL-CAT-PWY.ttl
models/ALANINE-DEG3-PWY.ttl
models/ALANINE-SYN2-PWY.ttl
models/ALL-CHORISMATE-PWY-1.ttl
models/ALLANTOINDEG-PWY.ttl
models/ARG-PRO-PWY.ttl