fall_2020_log

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

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

Works Trying again with more imports:

bcodmont.yaml

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

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