yochannah

This is a set of commands that I use when testing PRs, bugfixes, etc.

Deploying a mine

This is done from inside a checked-out mine folder, NOT the InterMine folder

First deploy - stacktrace is optional.

./gradlew cargoRedeployRemote --stacktrace

yochannah

(def props {:version "0.9.4-SNAPSHOT"})

(defproject org.intermine/bluegenes (:version props)
  :dependencies [; Clojure
                 [org.clojure/clojure "1.9.0"]
                 [org.clojure/clojurescript "1.10.145"]
                 [org.clojure/core.async "0.3.443"]

                 ; MVC
                 [re-frame "0.10.2"]

yochannah

(def props {:version "0.9.4-SNAPSHOT"})

(defproject org.intermine/bluegenes (:version props)
  :dependencies [; Clojure
                 [org.clojure/clojure "1.9.0"]
                 [org.clojure/clojurescript "1.10.145"]
                 [org.clojure/core.async "0.3.443"]

                 ; MVC
                 [re-frame "0.10.2"]

yochannah

{
  "model": {
    "package": "org.intermine.model.bio",
    "classes": {
      "ChromosomalDuplication": {
        "extends": ["ChromosomeStructureVariation"],
        "references": {
          "sequenceOntologyTerm": {
            "displayName": "Sequence Ontology Term",
            "name": "sequenceOntologyTerm",

yochannah

best viewed in the swagger editor

yochannah

Keybase proof

I hereby claim:

• I am yochannah on github.
• I am yoyehudi (https://keybase.io/yoyehudi) on keybase.
• I have a public key ASDD6uhffR956xpmWI1COGfZpS37md_MM5wJMeu_36jnQAo

To claim this, I am signing this object:

yochannah

1. export tool sends user to splash page. maybe can model on flymine tool
2. splash page:
   1. is passed the url details for what it needs to fetch from galaxy.
   2. uses the registry to present a list of intermines to user, maybe with some
   3. user clicks on the one they want to take their galaxy workflow to.
   4. the splash page constructs the correct POST request to take the user to a portal link - I think the very first post example here
3. User is now happy and has what they need!

yochannah

OBF site redesign plans

Goal

Modernise the current site design, including the OBF logo, for a more professional front, allowing community members to more easily find info & contribute.

Method

Ideally an Outreachy intern, with web development and design skills.

yochannah

Problem:

The InterMine NLP project aims to create a tool that can take natural language and produce an InterMine query from it. In order to do this, we need examples of InterMine queries alongside their descriptions! Jake, our GSoC student working on this problem, is using InterMine templates (that's a FlyMine link - your preferred mine is equally valid though!) from the various InterMines as a starting point, but more examples would be better if possible (and produce better results!).

Can you help us make more?

Do you have any personal saved queries or templates from your mine that you could share with us, alongside a description of what the query is? Or maybe you have some interesting biological questions you could answer in InterMine and want to share with us?

Example

Description of query: Show genes located on a particular chromosome.

yochannah

Good Query

This query is the same as the bad query below, but note the constraint code code=c("B").

 im <- initInterMine(mine=listMines()["HumanMine"])
 queryGeneOrth = getTemplateQuery(
     im = im, 
     name = "Gene_Orth"
 )
 newConstraint &lt;- list(