Working IMS

[Gray, Alasdair J G]

Hi

Is there a working deployment of the IMS that we can use? Unfortunately the Open PHACTS deployment has been taken offline.

We are wanting to discover sets of equivalent IRIs when we don’t know the original species or even the type of the IRI, which means the BridgeDb service is not an option for us.

Alternatively, is the IMS in a state that it is easily deployable with the linksets that would be used to support Wikipathways?

Thanks

Alasdair

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Alasdair J G Gray

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Heriot-Watt University, Edinburgh, UK.

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[Egon Willighagen]

Dear Alasdair, all,

On Mon, Jul 22, 2019 at 9:11 PM Gray, Alasdair J G <A.J.G...@hw.ac.uk> wrote:

Is there a working deployment of the IMS that we can use? Unfortunately the Open PHACTS deployment has been taken offline.

No, but we recently wrote up how to fire it up: https://f1000research.com/articles/7-1390/v1

This paper (has been reviewed, and rejected) needs work. The amount of data is grown immensely and cannot be served as a Derby file yet.

But the paper also has a IMS section, and we wrote up this tutorial: https://github.com/BiGCAT-UM/BridgeDbVariantDatabase/blob/master/Local_BridgeDb_IMS_installation.md

And my SWAT4HCLS paper from last December also uses this exact same set up.

Now, it turns out that the IMS depends on an older MySQL version and that the BridgeDb code has not been updated for a recent MySQL change where they changed how to store passwords. Getting the MySQL have the right user/password combo is a bit of a pain, and while I managed twice, I have not been able to find a reproducible way.

Basicallly, the BridgeDb IMS stack needs updating. Nuno has also been looking into this.

 

We are wanting to discover sets of equivalent IRIs when we don’t know the original species or even the type of the IRI, which means the BridgeDb service is not an option for us.

Clear. Yes, there are plenty of essential, unique IMS use cases.

 

Alternatively, is the IMS in a state that it is easily deployable with the linksets that would be used to support Wikipathways?

The WikiPathways website? There we don't use IRIs and a "regular" BridgeDb webservice is enough.

Egon

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[Gray, Alasdair J G]

Egon, thanks for the response.

On 23 Jul 2019, at 09:23, Egon Willighagen <egon.wil...@gmail.com> wrote:

On Mon, Jul 22, 2019 at 9:11 PM Gray, Alasdair J G <A.J.G...@hw.ac.uk> wrote:

Is there a working deployment of the IMS that we can use? Unfortunately the Open PHACTS deployment has been taken offline.

No, but we recently wrote up how to fire it up: https://f1000research.com/articles/7-1390/v1

This paper (has been reviewed, and rejected) needs work. The amount of data is grown immensely and cannot be served as a Derby file yet.

But the paper also has a IMS section, and we wrote up this tutorial: https://github.com/BiGCAT-UM/BridgeDbVariantDatabase/blob/master/Local_BridgeDb_IMS_installation.md

And my SWAT4HCLS paper from last December also uses this exact same set up.

Now, it turns out that the IMS depends on an older MySQL version and that the BridgeDb code has not been updated for a recent MySQL change where they changed how to store passwords. Getting the MySQL have the right user/password combo is a bit of a pain, and while I managed twice, I have not been able to find a reproducible way.

Basicallly, the BridgeDb IMS stack needs updating. Nuno has also been looking into this.

This sounds like something that my new Research Software Engineer could get started on as part of the FAIR+ project. I think that the IMS is an important technology for the interlinking of datasets and that we should do this in the context of developing a recipe for the cookbook. Edward starts on the 1 Aug so this could be his task for getting to know the BridgeDb framework.

 

We are wanting to discover sets of equivalent IRIs when we don’t know the original species or even the type of the IRI, which means the BridgeDb service is not an option for us.

Clear. Yes, there are plenty of essential, unique IMS use cases.

 

Alternatively, is the IMS in a state that it is easily deployable with the linksets that would be used to support Wikipathways?

The WikiPathways website? There we don't use IRIs and a "regular" BridgeDb webservice is enough.

This is related to the work my PhD student (Imran) is doing with Nanopublications. We are extracting the topics from the Wikipathways nanopublications which gives us IRIs. We then want to expand those to the set of equivalent IRIs. Since we are using Wikipathways, we want the link sets that are used in the regular BridgeDb web service, but our starting identifier is an IRI which we do not know the type of.

Best regards