How to get Rightfield metadata into Seek

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Niels Zondervan

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Nov 28, 2017, 7:02:35 AM11/28/17
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Dear all,

When using RightField, there are nice tutorials on how to generate and fill in template files and how to export the meta-data as RDF or csv.
However, I am missing information on how to get metadata into Seek. I would expect that a RightField annotated file when uploaded would automatically get parsed for JERM metadata which shows up in Seek. This is however not the case (I tried it), any suggestions on how to get the metadata from RightField templates into public Seek?

Regards,

Niels Zondervan

Stuart Owen

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Nov 28, 2017, 12:05:47 PM11/28/17
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Hi Niels,

Thanks for your question regarding RightField and SEEK.

When we first created RightField, the motivation was to encourage people to use semantic controlled vocabularies within their data in a user friendly way, and also have this metadata encapsulated within the spreadsheet for others when they download them. This was all done in the context of SEEK, but also entirely free to use in other contexts and isn't SEEK dependent.

When templates are uploaded to SEEK, this metadata is extracted and included within the RDF (in a loosely coupled fashion). This is also available if setup together with a sparql endpoint. It was also always our intention that the templates would auto-populate the forms when uploaded. However, you are correct to recognise that the automatic form population isn't yet completed. This was largely due to other priorities and pressures that were required as part of our current and future funding obligations and oppurtunities.

I'm pleased to report though, that we have and are recently going through a period of revisiting and returning to the metadata facilities provided by SEEK. We have produced a new version 2 of the JERM ontology (http://jermontology.org), with which we have now embedded into our upcoming version of SEEK (1.5.0). We are also recreating a new set of updated and improved templates using the newer ontology. We will also be providing a sparql endpoint for https://fairdomhub.org

And also, a peice of work we plan for the following version (1.6.0) is the form filling that you expected to happen. This is  our top metadata related priority for our next development sprint (https://jira-bsse.ethz.ch/browse/OPSK-1476). Infact, the largest effort is changing the upload workflow to support the extraction and form-filling. Extracting and recognising the metadata is already in place from work we'd done previously.

hopefully this helps, and sorry for any confusion.

regards,
Stuart
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Niels Zondervan

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Dec 4, 2017, 4:53:23 AM12/4/17
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Dear Stuart,

Thank you for you quick response, please keep me up to date on any progress, especially on the development of new templates.
In the project I am working on, the MycoSynVac project, we are finally at a point that all groups are willing to conform to the use of JERM templates for all the omics data (which a vast amount, basically all existing omics data on Mycoplasma pneumoniae and Mycoplasma hyopneumoniae).
We plan to make and publish a clear use case on the full potential of using Righfield and Seek in a large scale Systems and Synthetic Biology project. We will use single and multiple sample Righfield template for all omics data for this project. All omics data files will be uploaded on their respective database linked to by Seek and linked to several models that are based on these data. We are also investigating possibilities to make the data itself linked which as far as I know will not be supported any time soon by Seek and RightField.
Do you have an estimate on when these new templates conform the JERM v2 will be available so I can communicate this with all partners within our project?
We planned to start begin 2019 with implementing the use of RighField templates within the project, it is therefore very important we have a clear time frame when these new templates will be available, so we can avoid losing the motivation and momentum in the project to invest time in the use of Seek and RightField.

Regards,

Niels Zondervan

Niels Zondervan

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Dec 5, 2017, 4:07:53 AM12/5/17
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My apology, I see I made type in the above response. We will start implementing Seek and Rightfield templates start 2018. That is why I am asking for an estimate of the time frame in which these templates will become available.

Regards,

Niels Zondervan

Stuart Owen

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Dec 6, 2017, 11:48:24 AM12/6/17
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Hi,

So I can't give an exact time-frame or release date. However, this work has currently started and is underway for our SEEK 1.6.0 release, expected early next year. (1.5.0 is already finished and will be released tomorrow). We already have a generic JERM v2 test template we will be working with. The template work is the main priority for this version, together with some extensions to the JSON API to provide write support. There are some refinements and mappings we plan to add to the JERM ontology, but I don't expect this to affect the progress.

My estimate would be for the end of January / early Feb, although a test version could probably be made available sooner.

I have set myself a reminder to update you on progress midway through of January.

thanks,

Stuart.

Niels Zondervan

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Dec 7, 2017, 3:55:05 AM12/7/17
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Hi Stuart,

Thanks for keeping me informed, I will communicate this within our project so we can adjust our planning accordingly. The Templates are for us also the main priority since many new experiments are planned for early next year.
Regarding the JSON API, some colleagues in my group have recently published a genome ontology (GBOL) which includes a Stack with a code generator to automatically generate Java and R API's for any ontology, as well as checks for consistency of the data entered via the API.
This might be interesting to have a look at for future developments.
http://www.gbol.life/
https://www.biorxiv.org/content/early/2017/09/05/184747

Regards,

Niels

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Stuart Owen

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Feb 7, 2018, 10:59:42 AM2/7/18
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Hi Niels,

Here is a short update on the template upload work progress.

So far things are going quite well, but a little slower than hoped. I'm now as far as splitting up the datafile registration into seperate upload step & metadata filling steps, along with RightField extraction of terms from the template. These are then used to automatically populate the metadata form, which has been split up into 4 distinct steps, and it is possible to jump straight to the end.

Further work for the next release includes the ability to create an Assay, rather than select an existing one, during the upload process. This can either be done manually, or driven directly from the template. The UI of the stepss still needs quite a bit of tidying up, and the initial template still needs a bit of work.

For the version included in the next release, it is likely that it will only work with specific templates that we provide.

I'm afraid I can't give a specific date for the next release, but no new major features are planned to be started for it and it is mainly finishing off current tasks and fixes.

There is some future work needed for the templates, to make them more flexible and better defined, which requires enhancements to RightField. This will provide the ability to give certain cells some context - for example to say an identifier belongs to a Project or Assay class, or to say that a set of fields describe a new Assay. We are currently having to work around these limitations in a less than desirable way, which is why the initial version will only work with our specific templates.

regards,

Stuart

Niels Zondervan

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Feb 8, 2018, 3:51:37 AM2/8/18
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Hi Stuart,

Thank you for updating me. These are all behaviour that will make working with Seek RightfField a lot more intuitive and automated and will increase its l use. I can imagine it takes some time to perfect.
Are there already new template RightField files available, or can we use the old ones?
Some of our partners are now working on auto generating transcriptomics RightField enabled files within their pipeline so it would be best to settle as soon on the temple they have to use?

Regards,

Niels
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