GOlorize and BinGO plugin not working with new format association files version GAF 2.1

[Nancy Campbell]

Hi,
I seem to be unable to use the new version of GAF2.1 gene association files (annotation files) as downloaded from QuickGO, with GOlorize and BinGO. Has anybody found a workaround? Everythings works fine with version GAF v2.0.

I would assume this is related to the following format change in column 8 explained below (quoted from this web page http://geneontology.org/page/go-annotation-file-gaf-format-21):

"Changes in GAF 2.1

GAF 2.1 allows the use of pipes (|) and comma (,) in column 8 (with/from column) compared to GAF 2.0 which allows the use of pipes only. Pipe will indicate 'OR' and Comma will indicate 'AND'.

In GAF 2.0, multiple values are separated by pipes where the pipe has been used to mean 'AND'. However, in the annotation extension field (column 16) pipe is used to indicate 'OR' and a comma to indicate 'AND'. This change to column 8 will allow consistent use of pipes and commas in the GO annotations. Please see the descriptions below for full details."

Thanks

Nancy

[Nancy Campbell]

By a process of trial and error, I found what the problem is and how to solve it:
 
This file with this name works: gene_association_filter.goa
 
This does not work: goa_human_ftp.gaf ( no matter what extension is used such goa_human, txt, goa etc.).
 
So I tried
 
gene_association_ftp.gaf and lo and behold it works.
 
So the conclusion is that the presence of goa_human as part of the file name itself will stop the file working. However, goa_human is allowed to be part of the file extension.
 
There  you have it …..

[Nancy Campbell]

Hi,

I have done a bit more digging and it seems that GOlorize and BinGO assume a particular naming convention for files rather than accepting any file name and just verifying that it is the correct type by looking at the content.

So I will share here what have worked for me:

Cytoscape plugins GOlorize and BinGO will not be able to use the downloaded files with their current names for files released since June 2016 which coincides with release 158 and above. A typical file name format that will work looks like this:

gene_association.goa_human.164

where 164 is the release number.

In general , the file and its extension must follow these rules:

1. the expression "gene_association" must exist in the file name.

2. the expression "goa_human" must exist in the file extension.

Other combinations can work too. However, we have not tried them all and we can only advise that the above combination will work.

On Monday, 6 February 2017 13:43:10 UTC, Nancy Campbell wrote:

[Barry Demchak]

Hi, Nancy –

 

I’m sure the user community appreciates your digging. It seems like you’ve found information worth posting on the GOlorize User Guide wiki page and the BiNGO User Guide / Tutorial.

 

Do you agree? If so, we can involve the authors with this, too.

 

Thanks!

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[Benno]

Dear Nancy,

Thanks for figuring this out; unfortunately, at this time we don’t have a person to update the GOlorize App.

For now, I have posted a link to your post on the GOlorize Wiki. If you (or any other person) would like to look into updating GOlorize, we’ll be happy to facilitate.

Best regards,

—Benno Schwikowski

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[Nancy Campbell]

Hi Barry & Benno,

I think Benno's link to their GOlorize wiki is a good idea. Though I think this is a BinGO specific thing. But I agree since GOlorize uses BinGO, it is a very good idea to add the info on GOlorize documentation too.

I have also written to the BinGO developers separately and waiting to hear back.

BinGO website does allude to the approriate name of the annotation files but not directly. It says: "....Any file named gene_association. ... is handled as a GO Consortium annotation file by BiNGO." here is a link to the web page https://www.psb.ugent.be/cbd/papers/BiNGO/Customize.html

This worked fine when the Gene Ontology consortium used to name their files gene_association..... . However, only recently (since june 2016 which coincides with release 158 of these files, the naming has changed and it starts with goa_human..... which definitely does not work as is). I know it is a small thing but it is so small that it took some time to realise this really was the problem and how to solve it. Finding what the issue is is sometimes harder than addressing the issue!! :-)

What is not mentioned anywhere (well at least I could not find anything) that states very clearly that due to change of naming of files, then you must rename your file .... etc.

Thanks

Nancy

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[Barry Demchak]

Hi, Nancy –

 

You raise very good points, and your work to clarify the situation is very much appreciated.

 

This is an important issue and is getting our attention. We’ll discuss this in our weekly meeting, which is this morning. Please stand by.

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[alex.pico]

Hi Nancy,

Just catching up on this thread...

I assume there are no issues with latest ontology OBO files. The ones from here seem to work fine:
http://geneontology.org/page/download-ontology

But when it comes to annotation files, some resources are still providing the old "gene_association.xxx" files (which work fine), while others have "upgraded" to GAF files (which do not work):
http://www.geneontology.org/page/download-annotations

I opened up a working gene_association.sgd file and compared it to the latest, not-working goa_human.gaf. Other than the header, I could not see a difference that is relevant to BiNGO. So, I copy/pasted the header (all the lines starting with an exclamation point) from the .sgd file to the .gaf file and then renamed it, gene_association.goa and it worked!

I'm assuming at this point that BiNGO is doing some sort of check on the header that is causing this, but as long as the data columns are the same, this header-switch strategy should work.

If you are working with a GAF file that actually has different columns, then you'll have to rearrange them, e.g., in Excel, and then replace the header and save as a new filename.

These are my workarounds so far... Hope it helps!
 - Alex

[bif1...@student.lu.se]

Hey All,
I know its an old thread but I hope some of you are still active. I have a similar error working with BiNGO. I have been stuck on this for weeks now and I have been able to rule out any possible manual error on this. So this is what I have.

I am using the latest version of ontology file which downloaded from gene consortium and I have created the custom annotation just exactly as they have mentioned in the BinGO customize page. I submit with my list of input genes and submit. It doesn't execute and I see this on my taskbar.
"Task (bingo.internal.AnnotationParser@2c6a9732) title: Parsing Annotation "
This is not the first time for me working with BiNGO. I have previously successfully analyzed custom datasets. However, none of my troubleshoots worked this time. I came across some more post about the format, the first line, the gaf version, etc, I have tested more than two dozen combination, nothing works. I have checked my version, my java scripts and everything else seems to be alright.

I tested the version for demo dataset and it works. Just not my custom annotation. I was able to rule out the possibility for having a corrupt annotation file by testing my previous annotation file which was successful.

Any suggestion, any idea, any advice. I would be very happy to hear anything. Thanks.

[Matthew Rich]

I have this same issue. Has anyone solved this?

[Scooter Morris]

Hi Matthew,

  There is a new developer working on BinGO, so stay tuned...

-- scooter

[Rolf Lohaus]

Hi,

This issue should now be fixed in the latest BiNGO version (3.0.4).

Best,

Rolf

[Rolf Lohaus]

Hi Matthew,

This issue should now be fixed in the latest BiNGO version (3.0.4).

Best,

Rolf

[graham...@gmail.com]

I am attempting to use BiNGO 3.0.4 with a custom .obo and annotation file per the documentation.  The contents are KEGG pathway (this is mentioned as an example of something one might want to do for custom annotations).  Yet, I cannot get BiNGO to parse the files.  Question:  Is the documentation up to date and are the following formats correct?  What should these files be named?  The .obo and annotations look like this:

(curator=KEGG)(type=pathway)

00001 = Kegg_Pathway

09100 = Metabolism [isa: 00001 ]

09101 = Carbohydrate metabolism [isa: 09100 ]

00010 = Glycolysis / Gluconeogenesis [isa: 09101 ]

...

(species=Mus musculus)(type=KEGG_pathway)(curator=KEGG)

Ras = 02020

Egf = 02020

Tgfa = 02020

Fgf1 = 02020

Fgf2 = 02020

Fgf3 = 02020

The error is:  Could not load full ontology file: path/kegg.obo file could not be read or parsed

I have tried renaming the file to no avail.

BiNGO does run on local GO files as well as downloaded ones just fine.

Any help much appreciated!

Best,

Graham.

[manuel....@idener.es]

I have also a similar case! Any answer it would be appreciated. I have also tried to configure an entire .obo file comprising KEGG pathways, and it is not recognized either (even considering it was recognized by OBO-Edit).

Please, keep me updated!

Manuel.