Nov 2 release extra " in header?

[ybradford]

Hi Lynn,

Alliance technical was trying to load the Nov 2 file and finds that there are extra " in the header that will break the loader. Here is the stanza we think problem originates from (from diff file): subsetdef: DO_AGR_slim ""DO_AGR_slim"" subsetdef: DO_cancer_slim ""DO cancer slim"" subsetdef: DO_FlyBase_slim ""DO_FlyBase_slim"" subsetdef: DO_MGI_slim ""DO_MGI_slim"" subsetdef: DO_rare_slim ""DO_rare_slim"" subsetdef: GOLD ""GOLD"" subsetdef: gram-negative_bacterial_infectious_disease ""gram-negative bacterial infectious disease"" subsetdef: gram-positive_bacterial_infectious_disease ""gram-positive bacterial infectious disease"" subsetdef: NCIthesaurus ""NCIt"" subsetdef: sexually_transmitted_infectious_disease ""sexually transmitted infectious disease"" subsetdef: tick-borne_infectious_disease ""tick-borne infectious disease"" subsetdef: TopNodes_DOcancerslim ""TopNodes_DOcancerslim"" subsetdef: zoonotic_infectious_disease ""zoonotic infectious disease""

Can you fix it please? Thanks! Yvonne

[lschriml]

Hello Yvonne, I would be happy to fix the file, Can you tell which file and the directory you download from ?

I’ll get it fixed tomorrow.

Cheers, Lynn

Sent from my iPhone

On Nov 8, 2018, at 6:31 PM, ybradford notifications@github.com wrote:

Hi Lynn,

Alliance technical was trying to load the Nov 2 file and finds that there are extra " in the header that will break the loader. Here is the stanza we think problem originates from (from diff file): subsetdef: DO_AGR_slim ""DO_AGR_slim"" subsetdef: DO_cancer_slim ""DO cancer slim"" subsetdef: DO_FlyBase_slim ""DO_FlyBase_slim"" subsetdef: DO_MGI_slim ""DO_MGI_slim"" subsetdef: DO_rare_slim ""DO_rare_slim"" subsetdef: GOLD ""GOLD"" subsetdef: gram-negative_bacterial_infectious_disease ""gram-negative bacterial infectious disease"" subsetdef: gram-positive_bacterial_infectious_disease ""gram-positive bacterial infectious disease"" subsetdef: NCIthesaurus ""NCIt"" subsetdef: sexually_transmitted_infectious_disease ""sexually transmitted infectious disease"" subsetdef: tick-borne_infectious_disease ""tick-borne infectious disease"" subsetdef: TopNodes_DOcancerslim ""TopNodes_DOcancerslim"" subsetdef: zoonotic_infectious_disease ""zoonotic infectious disease""

Can you fix it please? Thanks! Yvonne

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[lschriml]

Hello Yvonne, the DO subset files in our /src/ontology/subsets directory have all been fixed, with new files pushed to GitHub.

Thank you for pointing this out !! Cheers, Lynn

[ybradford]

@lschriml thank you for updating the subsets directory. Can you please update the main doid.obo file? There are still double quotes in the main doid.obo file in the HumanDiseaseOntology/src/ontology directory. This is the Nov 2 release updates to cell type cancer logical definitions https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.obo

see extra " in the header: format-version: 1.2 data-version: releases/2018-11-02 date: 11:02:2018 12:32 saved-by: lschriml subsetdef: DO_AGR_slim ""DO_AGR_slim"" subsetdef: DO_cancer_slim ""DO cancer slim"" subsetdef: DO_FlyBase_slim ""DO_FlyBase_slim"" subsetdef: DO_MGI_slim ""DO_MGI_slim"" subsetdef: DO_rare_slim ""DO_rare_slim"" subsetdef: GOLD ""GOLD"" subsetdef: gram-negative_bacterial_infectious_disease ""gram-negative bacterial infectious disease"" subsetdef: gram-positive_bacterial_infectious_disease ""gram-positive bacterial infectious disease"" subsetdef: NCIthesaurus ""NCIt"" subsetdef: sexually_transmitted_infectious_disease ""sexually transmitted infectious disease"" subsetdef: tick-borne_infectious_disease ""tick-borne infectious disease"" subsetdef: TopNodes_DOcancerslim ""TopNodes_DOcancerslim"" subsetdef: zoonotic_infectious_diseas

[lschriml]

Yes, we will get this updated. We have been working to gets these fixed via our Robot loading. The final tweeks are almost in place. Becky Tauber is leading this effort, it should be finalized shortly.

Cheers, Lynn

On Tue, Nov 13, 2018 at 4:16 PM ybradford notifications@github.com wrote:

@lschriml https://github.com/lschriml thank you for updating the subsets directory. Can you please update the main doid.obo file? There are still double quotes in the main doid.obo file in the HumanDiseaseOntology/src/ontology directory. This is the Nov 2 release updates to cell type cancer logical definitions https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid.obo

see extra " in the header: format-version: 1.2 data-version: releases/2018-11-02 date: 11:02:2018 12:32 saved-by: lschriml subsetdef: DO_AGR_slim ""DO_AGR_slim"" subsetdef: DO_cancer_slim ""DO cancer slim"" subsetdef: DO_FlyBase_slim ""DO_FlyBase_slim"" subsetdef: DO_MGI_slim ""DO_MGI_slim"" subsetdef: DO_rare_slim ""DO_rare_slim"" subsetdef: GOLD ""GOLD"" subsetdef: gram-negative_bacterial_infectious_disease ""gram-negative bacterial infectious disease"" subsetdef: gram-positive_bacterial_infectious_disease ""gram-positive bacterial infectious disease"" subsetdef: NCIthesaurus ""NCIt"" subsetdef: sexually_transmitted_infectious_disease ""sexually transmitted infectious disease"" subsetdef: tick-borne_infectious_disease ""tick-borne infectious disease"" subsetdef: TopNodes_DOcancerslim ""TopNodes_DOcancerslim"" subsetdef: zoonotic_infectious_diseas

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-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 801 W. Baltimore St., Room 659 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 lschriml@som.umaryland.edu