Cross-references to MBInfo
UniProt-GOA have received a request for QuickGO to link out to the MBInfo resource (example entry:http://www.mechanobio.info/topics/cytoskeleton-dynamics/go-0030027). The email is copied below.
Is this an appropriate resource to include as a cross-reference in the GO so that QuickGO and other tools can pick these up?
Sandra Orchard knows the curator and has said that MBInfo has existed for about 3 years and is funded by the University of Singapore.
One potential issue might be their use of GO ID in their URL.
"I would like to take this opportunity to introduce you to our site, MBInfo Wiki. MBInfo is a wiki-based educational resource on various cellular and molecular functions, explained in the context of mechanobiology, which bridges cell biology with physics, engineering and computational biology. The website is created by the Mechanobiology Institute, Singapore, which is a research institute within the National University of Singapore. You can find out more about the institute here: mbi.nus.edu.sg.
Although MBInfo has been in existence for quite some time now, we have recently carried out a revamp.
You may wish to take a look at our new site at www.mechanobio.info. The new site just went online a week ago and we are currently ironing some of the bugs – so our apologies if some links or tools do not work correctly.
The various topics of our resource are now structured around Gene Ontology terms. We will gradually introduce more descriptions that cover more GO Terms as the website grows. We chose to structure our descriptions around GO terms to better standardize the nomenclature used in our content, and improve the compatibility of our site with existing resources such as QuickGO. This has included using the GO IDs within our URLs.
For example one of our pages, titled “Lamellipodium” can be found at http://www.mechanobio.info/topics/cytoskeleton-dynamics/go-0030027. The related GO Term Lamellipodium Assembly can be found at http://www.mechanobio.info/topics/cytoskeleton-dynamics/go-0030027/go-0030032
We have already planned to link out to the QuickGo database from our pages via the 'Gene Ontology' links in the Protein InfoBox displayed on each page, however we feel there are opportunities for greater collaboration between the resources, whereby links to MBInfo pages can also appear on QuickGO.
This will allow users of your resource to gain access to detailed descriptions of some Biological Processes or Cellular Components, and provide some context for these GO terms, in this case, in the study of mechanobiology.
Before we began our redevelopment MBInfo attracted approximately 2000 unique visitors per week and we expect this to grow substantially now that we have redeveloped the site. We hope that through greater collaboration we will be able to provide a resource that is useful to researchers as well as students and educators.
We would be grateful if we could discuss this further, and get an idea on what we would need to implement on our site to enable direct linking between our resources.
I have included our Managing Editor, Dr. Steven Wolf, in this email.
Thank you and I look forward to your reply
Pre-meeting working groups
The timings aren't going to work out as it stands - let's discuss.
Still no news?
- In attendance: Judy, Suzi, Mike, Paul T., Jane, Rachael, David, Kimberly, Rama, Huaiyu
- March GOC Meeting
- AI:Suzi will send email to GO consortium mailing list to remind everyone to add items to the meeting agenda
- Details on exact schedule will be sorted out, but people should feel free to add topics for discussion to the bottom of the meeting agenda wiki page
- Already some conflicts wrt to the Saturday working groups meetings; will try to schedule so people can attend as many sessions as needed
- April BioCurator Meeting
- Reminder email about Feb. 14th deadline already sent
- Who from GO is attending?
- Rama would like to submit an abstract on the GPAD/GPI file format
- AI: Need to double-check with Chris about status of scripts for converting between annotation file formats
- AI: Suzi will check with Seth and Chris about making a validator available as a link from file submission page on website
- Other ideas are listed on the GO-managers wiki page, including:
- Enrichment analyses/tools
- MGI Phenotype2GO
- Apoptosis re-curation
- MBInfo Link Out
- MBInfo group approached GOA about linking out to their site from QuickGO
- Rachael feels the links might be more appropriate as XREFs in GO
- AI:Rachael will follow up with the group to see how many pages they have and what the information content is, i.e. do they have a critical mass of information? what value is added?
- Jane - since GO is so fluid, it's nice to actually have the XREF in the file, but we need to assess if it's worth the effort to add the XREFs to the ontology
- Paul T. and Huaiyu cited NCBI Link Out SOPs as a model for how GO may wish to handle these types of requests in the future
- Also, Paul and Huaiyu expressed some concerns about the URLs for this site - we would need a generic URL base, otherwise these links could be very hard to manage
- Roll-over Funds
- No word on this yet; Judy has been in contact with NHGRI, though
- miRNA Curation Guidelines
- Ruth expressed an interest in discussing miRNA curation at the Texas meeting
- Increasing amounts of miRNA data and it would be a good time to discuss what is currently curated (e.g., in plants) and what types of experiments and annotations could be made
- AI:David will organize a discussion on this, to include info on existing annotations, relations