thejacksonlaboratory / hpo-web

a web application to search and navigate the Human Phenotype Ontology (HPO)

Hpo

This project was generated with Angular CLI version 1.2.6.

Development server

Run ng serve for a dev server. Navigate to http://localhost:4200/. The app will automatically reload if you change any of the source files.

Code scaffolding

Run ng generate component component-name to generate a new component. You can also use ng generate directive|pipe|service|class|module.

Build

Run ng build to build the project. The build artifacts will be stored in the dist/ directory. Use the -prod flag for a production build.

Running unit tests

Run ng test to execute the unit tests via Karma.

Running end-to-end tests

Run ng e2e to execute the end-to-end tests via Protractor. Before running the tests make sure you are serving the app via ng serve.

Further help

To get more help on the Angular CLI use ng help or go check out the Angular CLI README.

hpo-web's Issues

coordinate prefixes

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

Auto-Complete suggestion

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

LOINC Integration

• 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.

Links missing

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?

Links for non-existent terms leads to funny behavior

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.

Local neighborhood is not clickable for me in Chrome on Mac OSX

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.

Display xref provenance

to be good citizens, these mappings should be attributed.

Allow download of (page-specific) annotations as tsv

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.

Navbar Verbiage

Looking for verbiage to put on the navbar- 3 items

News not show correctly - or I don't understand

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?)

"View All News" should direct to the latest news

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

Distinguish matched text from search string

like so

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

Very slow in Europe

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:

Search for Disease IDs

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

Nice to have: clarity on what is meant by number of decendants

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

Hide alt-ids

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.

Gene Associations for Orphanet

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.

Front-Page Carousel Enhancement

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

Make this repo public

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

Missing gene entry

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

JanusGraph Migration

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

For term & disease pages: Consider a higher level introduction to ease into annotation detail.

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:

Tool tip for hierarchy

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

Choose different example disease on HPO site

obophenotype/human-phenotype-ontology#3764

Search for synonyms! Important!

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

Navbar Icons

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.

News items links should be clickable

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.

Monarch / MONDO linkouts

We should roll this out in stages.

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

HPO-Web curie	Monarch curie	Monarch URL example
ORPHA:	Orphanet:	https://monarchinitiative.org/Orphanet:276413
OMIM:	OMIM:	https://monarchinitiative.org/OMIM:612242
NCBI Gene (numeric fragments only are displayed)	NCBIGene:	https://monarchinitiative.org/NCBIGene:6622

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

Navbar: add main actions, park others, promote search

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.

Uniprot viewer does not load

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

Create a clean homepage with search front and center, additional info below

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.

Update HPO logo

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

Entire Hierarchy Page

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

Monarch logo is squished (It is too narrow)

Should be:

Is currently:

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

Description of LOINC project for website

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

Search Result Matching Spacing

These search results do not make sense

Ensemble gene ID

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

thanks

Davide

Disease names clip the ids

Looking to peter for rules on clipping orphanet

Add summaries of diseases to disease page

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.

Make FAQ-items linkable

each question should have its own link.

Ontology update automation

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

ontology update - october

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

This involves deployment as well.

Publication Integration

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

Add "search in all results" to autocomplete menu

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

Typo

Repiratory System should be Respiratory System

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

Add a feedback button with link to github issues

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.

Male urethral meatus stenosis

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

Search Box Styling > 1600px

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

Various enhancements to association table

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.