Manager 19February2014

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AmiGO2 and New Website

  • Status of new website and AmiGO2 ? Do we plan to have the new site site ready for the SAB meeting in March ? What else do we need to have done before it's production-ready?

PDT: Any plan to perform user test for the website and get feedback?
Jane: There is a user experience team at EBI. We can ask them to help.
PDT asked whether they need to free up some resource to this.
Jane: Will chat with them next week
PS: They probably can just spend a day or even an hour on it to identify glaring issues, since they are experts.

GAF-to-GPAD/GPI Conversion Scripts

  • Are these publicly available? If so, where?

Chris: There are scripts available. Will check with Tony.

Follow-up from MBInfo

Dear Rachael,

My name is Steven Wolf and I am the managing editor for the MBInfo Wiki.

Firstly, thank you for taking the time to look at our resource and for considering our proposal for future collaboration.

Currently we have 50 pages that are mapped to GO terms. These range in size from around 500 words to over 5000 words. We also have a further 10 pages being prepared for the website and once we have established the website as a wiki to the scientific community we expect to increase that number substantially.

Using generic URLs may be possible and I will discuss this with our web application developer when he returns from his vacation (which will be in a couple of weeks). We had hoped that we could obtain DOIs, or a similar indexing tool, for specific webpages however this does not appear possible. eISSN and other forms of registration appear to be website wide only. So we are still working on this solution.

The use of topics is needed as we are primarily an educational resource and a wiki (a wiki in the sense that anyone can log in and edit the site content, however all edits are vetted by the editors and PIs here at MBI before being integrated into the site). All biological processes and components are discussed within the context of 4 main topics (Cellular Organization, Cytoskeletal Dynamics, Mechanosignaling and Synthesis).

In some cases our pages cannot be mapped to a GO term as a suitable GO term does not exist. For example, http://www.mechanobio.info/topics/cytoskeleton-dynamics/go-0071437/Invadopodium-Assembly. In this case there is no Biological Process for Invadopodium Assembly.

Similarly, there are no GO terms related to mechanotransduction as a biological process. Given MBInfo describes processes relevant to mechanobiology, (any process or component that results from or contributes to mechanical force detection and transduction) we expect to encounter more instances where a lack of suitable GO term leave us having to use our own page naming. That said, in most instances we look for parent GO terms and write the information under these broader terms. This is done as long as it matches the overall style and structure of the site.

Thank you and I look forward to more discussion on this in the future.


Rachael: Their url is stable, but not generic.
PDT: Makes sense to come up with NCBI Linkout type of format, and ask them to maintain it. They can also do url redirect. Such format can also support other resources in the future.

PDT: It is 50 pages, so we don’t have a lot to gain. There is not a lot traffic coming from that resource. So we have to consider the cost to us.
Jane: How about xref.
Chris: Three options to do this. 1. Use xref and direct link to their webpage. 1. Creating a generic url. 3. Linkout mechanism.
Rachael: For xref, where to display the information.
Chris, They do the initial mapping, we can put them on a separate page.
Rachale, it is neater to have a generic url. If they can’t do it, then use xref method.

Texas Meeting Agenda

PDT: Flush out the agenda for the Texas meeting. A good place to start is for each working group to consider reporting the progress and remaining issues. Managers of each of those groups should decide what they want to report. Please submit to the agenda the topic and the time needed for the report.
PS: progress report, and then the issues for discussion, or decisions. Depending on the time availability, there maybe some negotiation later.
Rachael asked the question about the pre-meeting working groups for Saturday. Multiple working groups scheduled all day on Saturday. People fly in on that day. It will be good to have some clarification on them, so poeple can decide which on to go.
Chris: The idea for MoMo group is for the LEGO modeling. Maybe break down to specific topics to discuss, so people can decide when and where they want to be.