[InterMine Dev] OBO files and annotation

Paulo Nuin paulo.nuin at gmail.com
Mon Jul 23 20:52:57 BST 2018


If you notice from my previous email, the Anatomy Annotation GAF file doesn’t annotate genes and/or proteins like the GO-Annotation module. Is it possible to change the module to annotate Anatomy Term elements instead (WBbt: IDs)?

I can load the GAF file fine, but not surprisingly I am getting an error when I try searches. I can see on catalina.out this error:

query: <query model="genomic" view="AnatomyOntology.synonyms.name AnatomyOntology.identifier AnatomyOntology.name AnatomyOntology.description" sortOrder="AnatomyOntology.synonyms.name ASC" ></query>
format: json
java.lang.IllegalArgumentException: No simple name for class: AnatomyOntology,GOTerm

Our latest code is on the branch im-265 on Github.



> On Jul. 9, 2018, at 11:40 a.m., Paulo Nuin <paulo.nuin at gmail.com> wrote:
> Thanks Julie and Sam.
> Indeed our WB files are GAF2.0 format, so I am guessing just adapt the code for the regular GO Annotation step should be enough.
> !gaf-version: 2.0
> !Project_name: WormBase
> !Contact Email: help at wormbase.org
> WB      WBGene00000001  aap-1   Certain WBbt:0003679    WB_REF:WBPaper00005614  IDA     WB:Expr2275     A               Y110A7A.10      gene    taxon:6239      20180416
> WB
> WB      WBGene00000001  aap-1   Enriched        WBbt:0003679    WB_REF:WBPaper00030839  IDA     WB:WBPaper00030839:Larval_Pan_Neuronal  A               Y110A7A.10      gene
> taxon:6239      20180416        WB
> Probably the most important change would be the _keys.properties file. I am assuming the keys in the file are connected to each column in the file, is that correct?
> Thanks again
> Paulo
>> On Jun 29, 2018, at 6:28 AM, Sam Hokin <shokin at ncgr.org> wrote:
>> Hi, Paulo! Just FYI, I do my GO annotations in a post-processor, so in case you decide to do that (load the OBO and WB independently during integrate and then link them up in postprocess) here's an example:
>> https://github.com/LegumeFederation/legfed-bio-postprocess/blob/gradle/legfed-create-go-annotations/src/main/java/org/intermine/bio/postprocess/CreateGOAnnotationsProcess.java
>> I do it this way because I load genes from all over the place and felt that annotation is more of a post-process, linking GO terms listed in the gene descriptions with GO terms. (Yes, funky, but that's how we roll.)
>> On 06/26/2018 10:13 PM, Paulo Nuin wrote:
>>> Hi everyone
>>> We are trying to substitute on XML file that loads anatomy terms by an OBO file connected to an annotation one (extension WB for
>>> us). I was able to easily create code necessary to load the OBO file, but the annotation is turning a little bit trickier.
>>> Documentation is quite slim for this, is there any resource that would help me with this?
>>> Do we need to generate our own class or we can use a generic annotation loader? What is the preferred configuration strategy?
>>> Any help appreciated
>>> Thanks
>>> Paulo
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