sulab/wikigenomesbase

A configurable codebase for launching organism specific WikiGenomes spinoff applications (e.g. ChlamBase.org) This is a web application framework for creating a model organism database leveraging the taxonomic, genetic and functional data that has been loaded to Wikidata.org by the Gene Wiki Project.

ChlamBase.org

Genomic data portal to Wikidata.org built specifically for the chlamydial research community

ChlamBase.org, a fork of WikiGenomes.org, is an open source and user-curated database of functional annotations for 3 model Chlamydia species: C. trachomatis 434/BU ( LGV L2 ), C. trachomatis D/UW-3/CX, and C. muridarum Nigg. A primary goal of this portal is to provide a powerful user-oriented experience tailored to the research interests of the Chlamydia research community, and to the unique biology of Chlamydia.

A central feature of ChlamBase is to allow users to view, add, and edit: *evidence-based gene annotations *engineered mutant strains *orthologous gene comparisons *developmental gene expression *host interaction targets

Instructions to create a model organism database for the microbes of your choice, go to the wikigenomes_base repository and follow the build instructions.

Developer Notes

When cloning repo for first time:
pip install -r requirements.txt
Manually do pip install celery==4.0.0 afterwards (because it doesn't install properly in the requirements.txt file)
Copy secret_settings template and fill accordingly
Run server with python manage.py runserver

Need to install grunt in order to rebuild code
Install NPM
npm install grunt-cli -g
From chlambase directory, npm install
Then, do "grunt minify" to minify and rebuild classes

Also need to run ./setup in the JBROWSE directory
(Does not work on windows)
Need celery task manager: celery -A tasks worker --loglevel=info

wikigenomesbase's Issues

CC/MF/BP-specific review language

-refactor annotation review text templates to each GO domain

for all wizards, add a "Need help?" link

all boxes are constrained to wikidata items (for items, determination methods, mutation types, etc.) so we need to add something that says "Need help?" in case a user can't find the right term and needs to email us.

Add oauth token as optional access token in Wikidata

Localization Visualization module

-graphical visualization of the subcellular localization based on the cellular component go annotation

Quick download of sequence

Feature request :: Possible to add little links under Gene and Gene Product to quickly copy to clipboard (or open up a FASTA window) the particular sequence? Maybe also allow the user to do that under orthologs... That's something I (and presumably others) do frequently. Would save so many steps!

Missing names/root.json

Loading names.root.json is missing in JBrowse. I tried updating to JBrowse 1.14.1, and then ran bin/generate_names.pl for each taxon with and without the flag --hashBit 16, but the name generation script does not generate a complete name set and leads to more errors.

display mouseover evidence codes in Gene Ontology module

improve ortholog data

A joint effort has been discussed to create a robust ortholog table that includes evidence

Add PDB entries

-possible issues in identifier mapping with PDB and Uniprot/NCBI

Related publications form

Include form for adding publications that are relevant to current gene

Mutant Single Form Qualifier change - need confirmation

Changed P644[0].qualifiers.P2249 to P644[0].qualifiers.P1057 - is this correct?

Missing WD Item for CT_222

CT_222 is not found in WD even though its referenced here Q36281361
also update ortholog CTL_0475 to include CT_222

enhance cellular component annotation wizard to differentiate host vs bug

For example, a user may want to annotate a localization to "golgi", but that undoubtedly should refer to "host golgi". Our wizard should guide people...

Dojo loading failed

Loading failed for the <script> with source “http://127.0.0.1:8000/static/wiki/js/JBrowse-1.12.1/src/nls/dojo_en-us.js”.

see http://chlambase.org/organism/243161/gene/TC_RS00020

Loading Message on Ortholog Display

Bug: f[0] is undefined

in bootstrap.min.js:6:6886

align orthologs in display widget

set up https via letsencrypt

because the entire web is going https these days...

Syncing JBrowse with interface

When clicking on a gene feature in jbrowse the interface should redirect to that gene page.

manual review all annotations with curator WikiGenomes

need to be sure no test edits made it into wikidata....

Site name

Not really an "issue".

Keep as ChlamBase.org or change? Worthy of a discussion.. Most related portals seem to use ___base or ___db, so both ChlamBase or ChlamDB are appopriate. The chlamdb.org domain is also available. ChlamydiaBase and ChlamydiaDB are not as good – needlessly long. Any better ideas?

Fix wikidata query to include optional statements when getting cell component data

Several genes show "doesn't seem to be a gene in this genome" on main page

Example: see TC_RS00050 under Muridarum Nigg

faceting genes by different data types

Search results can be faceted based on data like expression timing and mutant availability

Change to "Your Email"

Cross-origin request blocked

Cross-Origin Request Blocked: The Same Origin Policy disallows reading the remote resource at http://enzyme.expasy.org/EC/4.2.1.24.txt. (Reason: CORS header ‘Access-Control-Allow-Origin’ missing).

see http://chlambase.org/organism/471472/gene/CTL0017

test issue before posting to GO issue tracker

This issue shows draft text to post on the GO issue tracker for input. Comments welcome, all but particularly @khybiske

---

In the context of a wikidata-backed project called Chlambase, we would like to annotate the localization of a set of Chlamydia proteins to various compartments in the host and in the inclusion body (which is the nucleus-sized structure indicated by the red arrow):

This table summarizes the localizations that our domain expert (@khybiske) has identified with example genes and references. We've also listed our best guess GO term with our confidence level in that guess.

Localization	Example Chlamydia Gene ID	Supporting PMID	Best guess GO	confidence level
host actin cytoskeleton	CT456	15199184	GO_0005884 or GO_0044163	low
inclusion lumen	CT049	18591235	GO_0020004 or GO_0043665	low
inclusion membrane	CT005	26416906	GO_0020005 or GO_0043664	low
host cell nucleus	CT737	20657819	GO_0042025	high
host cell cytosol	CT858	20522495	GO_0044164	high
host lipid droplets	CT163	16920627	GO_0044186	high
host cell plasma membrane	CT867	16824101	GO_0020002	high

And although we don't have any examples right at this moment, we will also be wanting to annotate Chlamydia proteins that localize to the host cell versions of peroxisome (GO_0005777), ER body (GO_0010168), and centrosome (GO_0005813).

Does anyone have input on these mappings, particularly if there are better mappings or cases where new GO terms could/should be created?

Fix Inclusion Body divs in svg

Will update as soon as the GO team responds

oauth authentication not working

No response to clicking "Authorize to edit" button in the upper right. Error message from console:

create a chlambase icon

Perhaps something based on one of these images?
https://www.google.com/search?q=chlamydia+pathogen&tbm=isch

If @putmantime and @khybiske can agree on one or a few representative images, we can get a graphics person to make it into a proper icon...

AppData not found in chlambase.org production

Only in the production version of chlambase we get the following error:

Ex: http://chlambase.org/organism/471472/gene/CTL0001

search chlambase by annotation features (GO, expression timing, etc.)

Challenging as the SPARQL queries become too big as more and more data is included in the request

Tn Mutants not showing up in JBrowse

Needs to be fixed by including in mutants gff file

build instructions

-create project build instructions and setup scripts to launch custom XBase instance

create a "Why Chlambase?" / About page

I think the site needs a page that explains what chlambase is about, and briefly lists its unique features and advantages over other gene-based databases. Looks like wikigenomes has an 'About' section. Something like that... but maybe more feature-driven. I can imagine encouraging some colleagues to explore the site, and it's not immediately obvious what chlambase can do that other sites cannot.

host pathogen interaction module

Identify other bacterial genes that interact with the same host entity.
Effectors etc.

Create WD Items for Elementary and Reticulate bodies

See here: https://www.ebi.ac.uk/ols/ontologies/bto/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_0001172

Use exact match: http://purl.obolibrary.org/obo/BTO_0001172

data validation on mutant annotation forms

-add reference base and coordinate constraints

create organism-wide activity feed

Data visualizations that report editing activity to organism specific items.

collect data on host cell localization

doesn't have to be complete, just enough example cases to show in paper.

reference not being recorded for new mutant annotations

data.data.results.bindings[0] is undefined

in controller/ctrl.$onInit/<@http://127.0.0.1:8000/static/wiki/js/app/go-form/go-form.component.js:12:36
and
controller/ctrl.$onInit/<@http://127.0.0.1:8000/static/wiki/js/app/operon-form/operon-form.component.js:15:36
and
TypeError: ctrl.currentGene.proteinQID is undefined[Learn More]
mainpage-view.component.js:86:29
TypeError: ctrl.geneQID is undefined[Learn More]
mutant-single-form.component.js:48:29
TypeError: ctrl.currentGene.geneQID is undefined[Learn More]

see
http://127.0.0.1:8000/organism/243161/gene/TC_RS00070

Add visualization of ortholog alignments

A cool feature would be to (in the Orthologs window) add a button that triggers a script/webapp(?) that aligns the sequences listed (maybe checkboxes for user to choose). At worst, this is a BLAST. But surely there must be better web functions for this, like clustal...?

show expression data for orthologs

Leaning towards showing expression timing for all orthologs in the expression timing box

Expression module

@putmantime What do you think about renaming the 'Expression timing' module to just 'Expression'. I can imagine putting under that (i) Expression timing (as you have now), (ii) Ortholog expression timing (as planned), (iii) EB or RB protein expression (data we can add during our TBD jamboree), (iv) Graphical representation of where the protein is secreted to (later).

Your thoughts?

look into journals to submit chlambase paper

Pathogens/ID/Microbiome options

• PLoS Pathogens
• Cell Host & Microbe
• Infection & Immunity
• BMC Microbiology
• Pathogens and Disease

Genomics options

• BMC Genomics
• NAR
• PLoS One

@khybiske @putmantime feel free to add others I've missed. My task is to look at if any of the pathogen-specific journals have software/tool article types...

add gene symbol to host-protein interaction table

UX suggestion

Easy one. Some users have mentioned they don't know what to do from the home page. I might suggest we somehow guide the user to click one of the 4 boxed genomes. e.g. color them, or put a fat arrow to the left of the tree...

update go terms in cell component visualizer to use new go terms

host cell peroxisome and host cell centrosome

enable comparison of genomic context to orthologs

Multiple genome comparison with orthologs aligned.
-likely multiple jbrowse instance stacked