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@apierleoni commented on Wed Jan 17 2018

make sure the package will install locally using a CI system

@emepyc commented on Thu Jun 29 2017

We need to make them more compact

@ElaineMcA commented on Wed Aug 15 2018

Issue moved to opentargets/library #28 via ZenHub

Finish developing the new UI to allow simple demos (eg. elastic)

It took me a while to find the search box, or where to start or move away from the welcome box.

It'd be much easier for a newcomer to have the search bar right in the middle of the page, more prominently displayed.

After doing one search and trying to do another one, it took me a while to see the 'x' on the top right corner of the page (below the github icon) to reset the results.

I kept clicking on the Library name next to Open Targets | hoping to reset the search results and take me back to the Welcome page.

It may be worth checking how many people struggle with that as I did.

We need to fix the name, this implies:

• Change the name of the repo
• Change the name of the graph and treemap npm components (currently prefixed with ots)
• Change the DNS (this will change the url we have already shared with early testers)

@emepyc commented on Thu Jun 29 2017

There is a way to zoom to a topic, but not a way to un-zoom it.
Probably the best way is when you click on an already selected topic

Also show the PMID in the details of the articles

gives no 'Muslim' or 'Pig' terms as when @apierleoni and @emepyc searched for my name (not sure if it's an issue with double quotes, single quotes or something else.

Tried "denise" AND "carvalho-silva" and got Ensembl and India only...

Not sure if it's clear that AND is case sensitive. It may be worth mentioning that. Perhaps we need a help page for this? Otherwise the Welcome box with the tips will become rather long?

@elipapa commented on Fri Sep 15 2017

in the platform

Looking at the example above, the papers should indeed reflect BRAF + what i clicked (gastric cancer).
However, I think most users would see the highlighting on the graph and think that the list of papers should include gastric cancer and pik3ca.

It may be solved by removing the highlighting from the nodes that connect to the one that you click.
The emphasis could be on the node and on hover on the edges/nodes that it connects to.

So a reload doesn't clear your current search.
For now we can encode only the query in the search box (and not the state of the filters).
We can add those as well if needed.

Affiliations?, keywords?
Also create buttons to add filters based on them

It's great to have the welcome note and instructions on how to perform the search.

Shall we add the feedback button on the right hand side as per other pages?
Or a link to [email protected]?

I also wonder if we need to say 'this site is currently under development'.
If it's beta, it's implicit to me it's not the 'final version' or a polished version...

In my view, everything single site is under development or better in constant development :)

@emepyc commented on Thu Jun 29 2017

We need to make them more compact

We need a way to undo steps or go back to previous searches.

@apierleoni commented on Wed Jan 17 2018

spacy v2 was release some months ago, and it delivered several important changes and improvements.
The important ones for this repo are:

• New models with smaller size and much improved performance
• Doc objects are now pickable
• Much improved support for vocabulary matching
• Ability to easily train NER models
• The new models run in a new NN backend, that is no longer able to release the GIL lock, but will load the models much faster
• customisable pipelines

There are breaking changes and the new models requires spacy v2.
The biggest change for this repo is the ability to pickle Doc objects. It means the current flow can be altered to have a function computing the Doc models and returning them for further processing later, allowing beam to scale spacy workers more efficiently.
Ideally docs to be processed should be send in batches so the workers can still improve it performances by loading the model just at init time.

other possible actions

• Use the spacy Matcher instead of pyahocorasick
• move all the custom text processing and the entity linking to a spacy customised pipe to speed up processing, and make the code more modular and easier to extend

and when done filter by date range and trend

It could be nice to keep the history of the searches stored somewhere and easily accessible (similar to what is available for the Batch Search tool i.e. previous lists are kept on the right hand corner with no need for future uploading i.e.

Is it WIP?

Or we believe this is not a use case?

This paper got missed out with the current Text mining pipeline and brought to my attention by the attendees of the Dundee workshop:

http://www.pnas.org/content/113/32/E4688.full

"Parkinson's" AND usp8 returns the aforementioned paper but not the search terms "Parkinsons" AND usp8. The latter terms in Google and EuropePMC return the paper (but PubMed does not).

Will the | Library support (some) synonyms?

http://targetvalidation.org/disease/EFO_0002508

@elipapa commented on Tue Mar 20 2018

• either make the aggs conditional, so that you can choose which one to run
• or make a count of the hits, if they are > 1M you put a sampler aggs in front of these aggs

in the meantime the webapp (cc @LucaFumis ) will do two calls: one to get papers and then another to get aggs/chips. That way the user does not see the spinning wheel of death.

@apierleoni commented on Tue Mar 20 2018

as in the platform, it is always recommended to make a call to get the data, and a separate call (with size=0) to get the agg data.
This allows for the real data to come quickly, and the aggs to pop up when/if available.

it will add a lot to the pubmed indexing and it will set library apart by making it more drug-development specific.

Is that link worth including? I'd say yes...

How about the links to the social media channels?
If you prefer the link to the email address instead of the Feedback button (#13), perhaps you may not want to have the links to social media either?

@emepyc commented on Thu Jun 29 2017

If you zoom in and click on the outer side of a node, this doesn' t fire the selection, if you drag the canvas the node is misplaced

The site is not displayed correctly on small screens