modify ebi_biomes.csv

[kaiiam]

Addressing PR #735 and issue #672 I have proposed the following changes. Please merge if correct or modify.

[pbuttigieg]

+1 for the link rather than the pseudopath

[cmungall]

much better!

I need to check if we need to uuencode spaces in the TSV, or whether this is taken care of at the OWL conversion level - can you post a snippet of the generated OWL?

[kaiiam]

compiling the ebi_biomes owl, the class renders as:

    <!-- http://purl.obolibrary.org/obo/ENVO_3100035 -->

    <Class rdf:about="http://purl.obolibrary.org/obo/ENVO_3100035">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ENVO_01000252"/>
        <rdfs:subClassOf>
            <Restriction>
                <onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002507"/>
                <someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ENVO_00000488"/>
            </Restriction>
        </rdfs:subClassOf>
        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A freshwater lake biome which is determined by a glacial lake. </obo:IAO_0000115>
        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://www.ebi.ac.uk/metagenomics/browse?lineage=root:Environmental:Aquatic:Freshwater:Ice:Glacial lake</oboInOwl:hasDbXref>
        <oboInOwl:hasNarrowSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glacial lake</oboInOwl:hasNarrowSynonym>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">glacial lake biome</rdfs:label>
    </Class>
</rdf:RDF>

@cmungall is this what you were expecting?

Should the space within the EBI path instead by handeled by a %20 instead of how I currently have it? i.e. http://www.w3.org/2001/XMLSchema#string">https://www.ebi.ac.uk/metagenomics/browse?lineage=root:Environmental:Aquatic:Freshwater:Ice:Glacial%20lake

[cmungall]

Can you replace the spaces with "%20"

…

On Fri, Mar 22, 2019 at 4:31 PM Kai Blumberg ***@***.***> wrote: compiling the ebi_biomes owl, the class renders as: <!-- http://purl.obolibrary.org/obo/ENVO_3100035 --> <Class rdf:about="http://purl.obolibrary.org/obo/ENVO_3100035"> <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ENVO_01000252"/> <rdfs:subClassOf> <Restriction> <onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002507"/> <someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ENVO_00000488"/> </Restriction> </rdfs:subClassOf> <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A freshwater lake biome which is determined by a glacial lake. </obo:IAO_0000115> <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://www.ebi.ac.uk/metagenomics/browse?lineage=root:Environmental:Aquatic:Freshwater:Ice:Glacial lake</oboInOwl:hasDbXref> <oboInOwl:hasNarrowSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Glacial lake</oboInOwl:hasNarrowSynonym> <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">glacial lake biome</rdfs:label> </Class> </rdf:RDF> — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#736 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AADGOa1Hmupntv27TtUlnARQqvZaamObks5vZWeegaJpZM4cC6Z8> .

[pbuttigieg]

Are we good to go with this merge @cmungall ?

[kaiiam]

Yes @cmungall if you don't mind weighing in, I'm unclear if I can / should change the this as it has the changes to envo-edit.owl from commit 2f04d9d, which @pbuttigieg merged in in another PR. Will git figure out that that commit has already been made and it will just ignore those changes? Or do we need to kill this PR and make my changes again. I don't know how/if you can get rid of specific commits on a branch.

[kaiiam]

I wanted to try and figure it out myself I ran git revert --strategy resolve <commit> which worked to get rid the unwanted commits, and now only the correct file is changed, however now were getting the This branch has conflicts that must be resolved issue. I tried running the instructions to fix it via the command line but I couldn't get that to work. Sorry if I made it worse, I just thought that removing changes to envo-edit.owl would fix the issue.

[cmungall]

Sorry not sure how best to resolve this.. if it isn't too much work, can you just do the dumb git thing. Copy the csv somewhere safe, close this PR, start a new one, and copy the csv over...?

[kaiiam]

Ya, no worries I suspected it may come to that. I'll do it that way, close this PR and make a new one.

[pbuttigieg]

It's strange, I'm seeing something like this over at SDGIO too : ghost commits emerging in new branches, originating from branches which were previously merged and deleted. I seem to be the common denominator here, so will also try to learn more about this. Perhaps it's a git/cygwin thing.

[pbuttigieg]

Yeah, conflicts have arisen due to a previous merge. Best to redo this, after I fix @rduerr PR #759

[pbuttigieg]

@kaiiam all done with PR #759 - will you be working on this in the next day or so? If not, then hold off on creating a new branch so other PRs can be formed without causing more conflicts.

[kaiiam]

Sure let me know when you finish, and I'll restart this PR.

[pbuttigieg]

Sure let me know when you finish, and I'll restart this PR.

Okay @kaiiam, all done. I'll wait for your new PR to be merged before starting any more.

[kaiiam]

Changes re committed in PR #763.