Manager 18December2013

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  • Email from the Transport Classification folks (Rama)
With my very limited staff, I curate the Transporter Classification Database (TCDB).  Our SAB has
 suggested that we use/develop an ontology for  TCDB based on the ChEBI and GO systems which we
 know collaborate with each other.  Currently we do not have an ontological system for TCDB at all,
 but we feel this is perhaps the most important advance we can make to improve our database.
 Within the Transport Biology Domain, we do not know of a unified system of ontology, although
 transport represents a major subdivision of both ChEBI and GO.  We want to take advantage of the
 expertise and progress made by the GO consortium rather than to reinvent the wheel, and apply it
 to TCDB.  For substrates of transporters as well as their chemical inhibitors and activators
 (modulators), we have been advised by our SAB that the ChEBI system may be be ideal.  For
 biological processes, we believe the GO system will be most useful and applicable.  In fact, in
 my NIH grant renewal proposal, currently in preparation, we consider this to be a primary goal.
 We would like to know if you would be willing to discuss this on Google Hangouts or Skype, or to
 in some other way communicate with us on the best procedures that we might use. Also, we are hoping
 you will be willing to provide a letter of support/collaboration for this purpose.  It is possible
 that our efforts with respect to transport systems could result in improvements in your ontology of
 biological substrates and processes. 

  • IDs for other object types

This is a follow up on the email thread about the other types of IDs we would like to curate, should we include annotations to complex IDs in the GAF, what happens to term enrichment etc..,_Monday,_December_9,_2013_5pm_GMT/12pm_EST/9am_PST#Minutes



Ontology editors (Jen) have previously worked with this group but had difficulties mapping between the two resources. The project fits with scope of GO but it would be good if we can get funding for the ontology development as we have so many other priorities. Need to ask them who is using their resource and where is it being applied Do they have the biological expertise? This will be useful for GO as we don't have expertise on transporters. Paul T., will schedule a call with the group, including Judy and ontology group.

Complex annotations GAF

There is a problem with including protein complex annotations in GAFs as the assumption by users is that all entities in the GAF are gene products. Chris would prefer to have a default GAF as we will for GOA reference files. The suggestion is to keep the complex annotations in GPAD and not include them in the GAF. We can put pipelines in place for submitting to the GOC in GPAD - advertise GPAD as including extra information, therefore more useful than GAF. We should send GPAD to PLOS as a mini-publication, but need to get together a few examples of GPAD usage, esp. complex annotation.

Cilia annotation

Jane and Rachael have had two skype meetings with Syscilia people. Cilia-related terms have been added by Paola and a P2GO tutorial given to the three curators by Rachael. Will spot-check annotations that come in. The Syscilia consortium have a meeting in January, Karen Christie is going as she is annotating mouse cilia project.

Synthetic biology project

Chris and Jane met with Trudi. This work is out of scope for GO but they want to annotate soon. Suggested using a non-GO annotation format and use this to generate an ontology afterwards. Use Phenote to capture annotations. Ask what their use case is and what they want to accomplish. We can give a letter of support for their proposal.

Migration of web content

Need to remind people to do this. Documentation needs to be clearer on linking to pages that are not created yet.


Servers have been set up by Stuart and Rama is testing.


Chris will produce architecture documentation for LEGO and related products