thejacksonlaboratory / hpo-web Goto Github PK

We would like to integrate HPO publications into zotero and access them via the rest api.

We are using material icons https://material.io/icons/.

If you'd like to use custom ones, please let us know where we can find them.

Put an INFO symbol near tree hierarchy and explain that we are showing only an excerpt of the entire HPO

Would it possible to add Ensemble Gene ID's mapping in the response of the API ?

thanks

Davide

Consider the following:

• Make the tab color the same as the column header row color (to clarify which tab is selected)
• Move the "view all" to the bottom of the table
• Increase font size of table title and headers (and the view all)
• If you are only including causal loss-of-function genes, I would recommend using 'causal genes' rather than 'associated genes' in the column header.
• Add linkouts to Monarch in final column
• Use MONDO disease IDs

cc: @mellybelly

Feedback welcome.

To the top of the autocomplete results, add "Search for in all results" so that the user immediately understands that they're not constrained to just the options they see in dropdown. This "all results" option should be preselected; downstream effect would be not different from the current behavior of user just pressing enter without selecting anything from dropdown

Repiratory System should be Respiratory System

see https://hpo.jax.org/app/browse/disease/ORPHA:8

to be good citizens, these mappings should be attributed.

Looking for verbiage to put on the navbar- 3 items

I know, I started it, but retrospectively I would say, let's not show the users the alternative IDs, unless they really want to see it. So I suggest to make a click-able thingy next to the primary ID that shows the alt-ids.

Migrate existing relational schema to a standalone implementation of JanusGraph using Tinkerpop/Gremlin

One reason to move away from the old browser was speed. However, currently loading a page like https://hpo.jax.org/app/browse/term/HP:0005144 takes over 10 seconds here. Is this a temporary issue?

See firebug analysis here:

• Create endpoint for getting LOINC information based on search.

• Create a controller that links the to the endpoint.

• Create a service (class) that will either query the db or get its information from an in memory bean and have it get called from the controller

• Create a view ( json blueprint ) for the controller to return

@pnrobinson Here are some basic steps to get the LOINC code information to the public site. I believe it would be in Aaron's best interest to implement these step to get to learn rest-apis.

Please let me know if this makes sense.

Please see here: monarch-initiative/dipper#469
@pnrobinson can you comment please?

On the page show here:

A link must be added for the files Genes_to_phenotype.txt and phenotype_to_genes.txt. They are not found under http://compbio.charite.de/jenkins/job/hpo.annotations/lastStableBuild/ .

There is another job that creates these and the link is : http://compbio.charite.de/jenkins/job/hpo.annotations.monthly/lastSuccessfulBuild/artifact/annotation/

Can you update this?

The HPO-Browser shows data for HERC1. Why is it missing here? Old data?

For instance,
https://hpo.jax.org/app/browse/term/HP:0000004

There is a progress symbol that never stops. Actually, HP:0000004 is an alternative id, and should map to the primary id. There is a function in phenol to do this.

Should be:

Is currently:

Please see the logos here; and use the stacked black version; thanks

Why is a search for "OMIM:160900" or "160900" not giving any results? The disease is there and can be found by the disease name. Is this intentional?

@pnrobinson @iimpulse

Update the ontology for an october release it's been a few months.

This involves deployment as well.

Update highlighting technique to be more in line with proper ui standards and make the output full width of the search plus the filter, fix the filter width to be like amazon.

I feel like we should be updating all references to "Terms" -> "Phenotypes" for example the heading of the category in autocomplete.

@jmcmurry @pnrobinson @drseb

Hi there; please update the HPO logo. There are various configurations to choose from here:
https://github.com/jmcmurry/closed-illustrations/tree/master/logos/hpo-logos

Looks abnormal above this pixel range. Will reduce size to bring it in line above this range.

While the dumps have now been linked (I think), there still needs to be a .tsv download option provided at the level of disease pages and term pages. The downloads (at a minimum, but perhaps also the UI) should explicitly state the provenance of the associations, even if this is exclusively showing those we have curated ourselves.

On tooltips etc, perhaps worth clarifying that the number is the number of direct descendants rather than just "descendants"?

We should roll this out in stages.

• Step 1. Link out using existing identifiers. (see #40)

• Step 2. Change the HPO Web DB back end to use MONDO IDs natively.

Add a short summary of diseases near the top of the page and above the list of HPO terms.
For instance, for Marfan syndrome, we could get these texts from
https://rarediseases.info.nih.gov/diseases/6975/marfan-syndrome
https://medlineplus.gov/marfansyndrome.html
http://www.uniprot.org/diseases/DI-00699
We will not be able to get texts for all diseases from these sources, so the Web app should regard this as optional.
@jmcmurry @mellybelly Does biolink have anything like this? If not, do you recommend any particular site as the best place to get this data. It is not obvious whether we will need to webscrape and if there are legal restrictions on the NIH data sources.

Leverage new instance of bamboo to create automatic update of the ontology and associations.

It doesn't have to be this per se. It depends on whether you want the emphasis to be the navigation or the data. But for discussion purposes:

obophenotype/human-phenotype-ontology#3764

Looking to peter for rules on clipping orphanet

I would have expected to be able to click to navigate between terms, but for some reason can not; I'm not sure if this has simply not yet been implemented yet?

Also, I can't find, offhand, a term with multiple parentage, so am curious to know how this is rendered in the neighborhood view.

The file "news.json" has one item for June 2018 (new release), but the website is not showing this item, but another one (Easy-to-use and secure deep phenotyping).

I added a July-item, which is not shown so far (is it a cronjob or how does it work?)

Now that this repo is public, please add a link to the GitHub issues from the UI.
I suggest adding "Request a feature / report a bug" to the FAQ. From there link to the hpo-web or hpo depending on what kind of issue it is.

Create a page to explore the entire HPO Hierarchy. Provide suggestion on the local term tree

Users always have to click on "View All News" to actually see the news. It would be cool if the items like "New HPO Annotation File Format" could be clickable.

The current Phenol class OrphaGeneToDiseaseParser should be able to parse the Orphanet file here
http://www.orphadata.org/data/xml/en_product6.xml
to get these associations.

like so

I also suggest de-emphasizing the identifiers. They can still be present, but perhaps in grey.

The browser must support a search for synonyms, e.g. there should be a match when I search for Short nose or one of these:

• Small nose
• Nasal hypoplasia
• Shortened nose
• Short nose
• Decreased length of nose
• Hypoplastic nose

Please check why this is not showing on the web app.

I suggest:

• Picking the three actions you most want the user to do, and make them main items on navbar. For instance, like so:

• Demoting "extract terms from clinical text." to a submenu under "other tools" [text mining can still be part of the diagnostic workflow]. I don't feel strongly about this specific item so much as pulling these main items into view.
• In all pages except the home page, promoting search to the navbar ; for instance, like so.

I'm not sure what is meant by "explore research data"; is this meant to link to Monarch? Please clarify.

Nothing happening when trying to load.

tried with https://hpo.jax.org/app/browse/gene/58484 and https://hpo.jax.org/app/browse/gene/81794

If I click on "View All News" it links to the news from April, although there are news items for May and June. It should link to the latest news per default

each question should have its own link.

Write a blog-like page with one or two graphics and a description of the LOINC2HPO project for the website.

I find this visually a bit cluttered the words "Human Phenotype Ontology" appearing 3 times.

Also, searching the corpus is most likely reason people come to the site so it should be promoted to homepage.

I suggest something more akin to what the homepage of OLS looks like. Strawman here.

Other ideas welcome; however, similar look feel to the eventual re-make of Monarch would be appreciated.

With the NAR paper coming up, we need this repo to be public so that folks can make tickets

It would be nice to enhance the "tools" section of the page with a rotating carousel, especially as more tools get added.

This can be a goal for hpo 2.0