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Kai Blumberg edited this page Nov 5, 2020 · 24 revisions

09.01

COB workshop:

http://ontology.buffalo.edu/bfo/SQU.pdf

https://github.com/obophenotype/upheno/blob/master/src/patterns/dosdp-dev/abnormallyFusedAnatomicalEntities.yaml

https://docs.google.com/document/d/1LuUENHEwe0lKrghSpDJb8q8FUkBVakuaeZU5Z0OjorY/edit

https://docs.google.com/document/d/1cX9uImaE103MRyXJ1gGXn4KN-rzocldISuCGWQ-vBPw/edit

cob-data-demo from James Overton

COB Workshop 2020 drive folder need to finish watching day 1 part 2 chemistry material.

COB UO ticket: https://github.com/jamesaoverton/cob-data-demo/issues/1

09.02

Login for lytic UA netID and pass:

ssh [email protected]


Use this: https://github.com/hurwitzlab/planet-microbe-functional-annotation/blob/master/singularity/recipe.def along with one of the hurwitz lab repo perhaps something called tacc-template that has a good skeleton by which to copy for the creation of a singularity image for the EBI pipeline that Matt M has now finished.

10.05

Links from NERC given from Mike Kittridge in this ENVO thread

https://www.bodc.ac.uk/resources/vocabularies/vocabulary_search/P01/

http://seadatanet.maris2.nl/bandit/browse_step.php

https://github.com/nvs-vocabs/P01

BODC presentation: https://github.com/nvs-vocabs/P01/blob/master/The_BODC_P01_PUV_semantic_model_Aug2019.pdf

physical parameter CV http://vocab.nerc.ac.uk/collection/S29/current/

chemical CV http://vocab.nerc.ac.uk/collection/S27/current/

10.06

Create BCODMONT via ODK:

Having issues on Mac, so I tried it on linux, which works.

git clone https://github.com/INCATools/ontology-development-kit.git

sudo docker pull obolibrary/odkfull

mv ~/.gitconfig/ ~/.gitconfig_backup_dir

vim ~/.gitconfig and paste in the following:

# This is Git's per-user configuration file.
[user]
# Please adapt and uncomment the following lines:
        name = Kai Blumberg
        email = [email protected]

now finally the odk example will run sudo ./seed-via-docker.sh -d po -d ro -d pato -u cmungall -t "Triffid Behavior ontology" triffo

Now to start BCODMO:

Make the file:

bcodmont.yaml and put it in ontology-development-kit/examples/bcodmo

id: bcodmont
title: BCODMO Ontology
github_org: BCODMO
repo: bcodmont
import_group:
  products:
    - id: ro
    - id: pato
    - id: envo
    - id: iao
    - id: obi
    - id: uo
    - id: uberon

sudo ./seed-via-docker.sh -C examples/bcodmo/bcodmont.yaml

####
NEXT STEPS:
 0. Examine target/bcodmont and check it meets your expectations. If not blow it away and start again
 1. Go to: https://github.com/new
 2. The owner MUST be BCODMO. The Repository name MUST be bcodmont
 3. Do not initialize with a README (you already have one)
 4. Click Create
 5. See the section under '…or push an existing repository from the command line'
    E.g.:
cd target/bcodmont
git remote add origin git\@github.com:BCODMO/bcodmont.git
git push -u origin master

BE BOLD: you can always delete your repo and start again

modified from the …or push an existing repository from the command line Note you can't add a readme or license (probably .gitnore either) otherwise you won't get to here and there will be a merge conflict when you try to push the ODK created material to the new repo.

cd target/bcodmont
sudo git remote add origin https://github.com/BCODMO/bcodmont.git
sudo git branch -M main
sudo git push -u origin main

Had previously tried with the bcodmont.yaml to be:

id: bcodmont
title: BCODMO Ontology
github_org: BCODMO
repo: bcodmont
import_group:
  products:
    - id: ro
    - id: pato
    - id: envo
    - id: iao
    - id: obi
    - id: uo
    - id: bco
    - id: pco
    - id: uberon
    - id: chebi
    - id: ncbitaxon

but it won't work, chebi and probably ncbitaxon are too big and might time out, will have to add manually like I did for CDNO.

EBI pipeline

added

export PATH=~/software/FragGeneScan1.3:$PATH

export PATH=~/software/Trimmomatic-0.39:$PATH

export PATH=~/software/my_interproscan/interproscan-5.44-79.0:$PATH

export PATH=~/software/pear-0.9.11-linux-x86_64/bin:$PATH

export PATH=~/software/vsearch-2.14.2:$PATH

to .bashrc on my EBI atmosphere VM and did source .bashrc to always add them.

Run with: python3 pipeline/pipeline.py -c ./data/configs/config.txt

Have to change: in the pipeline.py

self.trim_executable_fp = os.environ.get('TRIMMOMATIC-0.39.JAR', default='/home/u29/mattmiller899/Trimmomatic-0.39/trimmomatic-0.39.jar') the default to: ~/software/Trimmomatic-0.39/trimmomatic-0.39.jar

From Matt M: about singularity https://sylabs.io/guides/3.6/user-guide/build_a_container.html#creating-writable-sandbox-directories

EBI's view to get the data e.g. https://www.ebi.ac.uk/ena/browser/view/SRR1185413

10.07

the bootstrap is technically the header. It's what defines the core operating system in the singularity image. A sample recipe would look like:

Bootstrap: docker
from: ubuntu:16.04
%setup
### First thing to run after base OS is installed, can execute commands on local host environment or in the container
### These commands have sudo privileges so it can be dangerous for the host environment. I usually don't have this section
%files
### This gets files from the host environment and puts them in the container
%post
### This is where you download files from the internet and install software, packages, etc.
%test
### Tests to run at the end of building
%environment
### Define environmental variables used at runtime (not during build time, if you need environmental variables during building you have to define them in post, but the post environmental variables will be available during runtime)
%runscript
### Put code you want to run when you do "singularity run my.simg arg1 arg2" or "./my.simg arg1 arg2. Receives the options as $* (single string) or $@ (quoted array)
echo "Hello, world"

For Ocelote, you can't use anything newer than Ubuntu v16.04 (idk about other linux flavors or Puma). For learning singularity, you can build a sandbox directory ("test_simg/") from the above template recipe ("test.def") and go into it and install stuff by

sudo singularity build --sandbox test_simg/ test.def
sudo singularity shell --writable test_simg/

10.21

Need to write a new ESIP session call.

ESIP sem harm: Call for Sessions WM21

2021 ESIP Winter Meeting Session Proposal Form (Responses)

from brandon: https://github.com/ESIPFed/sweet/pull/225

10.27

ssh [email protected]

10.28

from bonnnie: phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes

10.30

Original PATO repo, made a fork of it kaiiam/pato

From this post on keeping fork up to date run the following in the fork:

#add upstream
git remote add upstream https://github.com/pato-ontology/pato.git

#check
git remote -v

#update
git fetch upstream

# merge can maybe also do: git pull upstream master
git merge upstream/master

Pato editors readme edit the pato-edit.obo file. Their conventions are to:

  1. put a database_cross_reference annotation property on the definition using type string.

  2. looks like they also add an id field with the curie of the purl (maybe an OBO thing)

  3. Some terms have a created_by I'll add my orcid

  4. Some terms have a creation date with iso date stamp.

Need to give myself an ID range will add it to my PR for issue https://github.com/pato-ontology/pato/issues/345. Will add the id range:

Datatype: idrange: 15
Annotations: allocatedto: "Kai Blumberg"
EquivalentTo: xsd:integer[> 70001 , <= 75000]

11.05

NERC meeting:

https://github.com/adamml/opm-owl

https://www.bodc.ac.uk/resources/vocabularies/vocabulary_builder/

https://www.bodc.ac.uk/resources/vocabularies/vocabulary_builder/matrix/

http://vocab.nerc.ac.uk/collection/S26/current/

https://www.bodc.ac.uk/resources/vocabularies/vocabulary_builder/bioentrf/

example the nerc term for atmosphere is https://vocab.nerc.ac.uk/collections/S21/current/S21S001

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