joeflack4
commented
2 years ago I changed the output format from .ttl to RDF .xml.
As for checking if it is parseable by ROBOT, I have some indicators of success, and indicators of failure.
Indicators of success
1. robot verify doesn't seem to have errors
2. robot convert doesn't seem to have errors
3. make omim_slurp doesn't runs without error, though has warnings
sh run.sh make omim_slurp
Running ODK with 8 GB of memory.
Makefile:1096: warning: overriding recipe for target 'reports/semantic-xref-pairs.tsv'
Makefile:535: warning: ignoring old recipe for target 'reports/semantic-xref-pairs.tsv'
cd sources/omim && make all -B
make[1]: Entering directory '/work/src/ontology/sources/omim'
curl https://github.com/monarch-initiative/omim/releases/download/latest/omim.xml --output omim-src.ttl
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 616 100 616 0 0 2006 0 --:--:-- --:--:-- --:--:-- 2006
owltools omim-src.ttl --set-ontology-id /mondo/omim-src.owl -o omim-src.owl
2021-10-05 17:24:27,773 ERROR (OWLOntologyID:82) Ontology IRIs must be absolute; IRI /mondo/omim-src.owl is relative and will be made absolute by prefixing urn:absolute: to it
echo "WARNING: OMIM ingest has multiple labels on classes (see https://github.com/monarch-initiative/dipper/issues/969)"
WARNING: OMIM ingest has multiple labels on classes (see https://github.com/monarch-initiative/dipper/issues/969)
robot convert -i omim-src.owl --check false -f obo -o omim-src.obo.tmp.obo && grep -v ^owl-axioms omim-src.obo.tmp.obo | perl ./bin/fix-omim.pl > omim-src.obo
rm omim-src.obo.tmp.obo
perl ../../obo-grep.pl --neg -r '(equivalent_to|is_a: SO|property_value: RO:0002524)' omim-src.obo | perl ../../obo-grep.pl -r 'property_value: https://w3id.org/biolink/vocab/category https://w3id.org/biolink/vocab/Disease' - | perl -npe 's@http://omim.org/entry/@OMIM:@g;s@http://www.omim.org/phenotypicSeries/PS@OMIMPS:@g' | perl ../../obo-grep.pl -r 'id: OMIM' - > omim.obo.tmp.obo
owltools omim.obo.tmp.obo --set-ontology-id http://purl.obolibrary.org/obo/omim.owl -o -f obo omim.obo && rm omim.obo.tmp.obo
owltools omim.obo --set-ontology-id http://purl.obolibrary.org/obo/omim.owl -o omim.owl
mkdir -p ../releases/v2021-10-05
cp omim.owl ../releases/v2021-10-05
make[1]: Leaving directory '/work/src/ontology/sources/omim'
robot --catalog catalog-v001.xml convert -i sources/omim/omim.owl -o mirror/omim.obo
wget --no-check-certificate http://purl.obolibrary.org/obo/hp.obo -O mirror/hp.obo.tmp && mv mirror/hp.obo.tmp mirror/hp.obo && touch mirror/hp.obo
--2021-10-05 17:24:35-- http://purl.obolibrary.org/obo/hp.obo
Resolving purl.obolibrary.org (purl.obolibrary.org)... 52.3.123.63
Connecting to purl.obolibrary.org (purl.obolibrary.org)|52.3.123.63|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo [following]
--2021-10-05 17:24:35-- https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.110.133, 185.199.111.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 7614919 (7.3M) [text/plain]
Saving to: ‘mirror/hp.obo.tmp’
mirror/hp.obo.tmp 100%[================================================================================>] 7.26M 3.09MB/s in 2.4s
2021-10-05 17:24:38 (3.09 MB/s) - ‘mirror/hp.obo.tmp’ saved [7614919/7614919]
cat mirror/omim.obo | perl ../scripts/add-to-tbd.pl > tmp/tbd_omim.tbd
READING mirror/hp.obo
READING mondo-edit.obo
READING omim-exclusion-set.obo
READING NEXT
Use of uninitialized value $xref in pattern match (m//) at ../scripts/add-to-tbd.pl line 295, <> line 3.
Use of uninitialized value $xref in concatenation (.) or string at ../scripts/add-to-tbd.pl line 295, <> line 3.
Use of uninitialized value $name in concatenation (.) or string at ../scripts/add-to-tbd.pl line 295, <> line 3.
cat tmp/tbd_omim.tbd | perl ../scripts/obo-grep.pl --neg -r ALREADY - | perl ../scripts/obo-grep.pl --neg -r is_obsol - | perl ../scripts/obo-grep.pl -r "xref: OMIMPS" - > tmp/ps_slurp_omim.obo
cat tmp/tbd_omim.tbd | perl ../scripts/obo-grep.pl --neg -r ALREADY - | perl ../scripts/obo-grep.pl --neg -r is_obsol - | perl ../scripts/obo-grep.pl -r is_a - | perl ../scripts/obo-grep.pl --neg -r "no mapping" - > tmp/rest_slurp_omim.obo
sed -i -E 's/is_a[:][ ]MONDO[:]0000001[ ][{]source[=]["]OMIM[:][0-9]+["][}][ ][!][ ]disease[ ]or[ ]disorder/is_a: MONDO:0003847/g' tmp/rest_slurp_omim.obo
echo "Slurping of omim completed".
Slurping of omim completed.
rm tmp/tbd_omim.tbdIndicators of failure
1. Outputs of make omim_slurp are roughly empty
cat tmp/ps_slurp_omim.obo
xref: {source="MONDO:equivalentTo"} !
cat tmp/rest_slurp_omim.obo
xref: {source="MONDO:equivalentTo"} !
matentzn
Description
@matentzn wrote: