minerva2rdf

Code base to convert Minerva models to WikiPathays WPRDF.

https://github.com/egonw/minerva2rdf

Science Score: 44.0%

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
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Scientific vocabulary similarity
Low similarity (4.8%) to scientific vocabulary

Last synced: 10 months ago · JSON representation ·

Repository

Code base to convert Minerva models to WikiPathays WPRDF.

Basic Info

Host: GitHub
Owner: egonw
License: mit
Language: Groovy
Default Branch: main
Homepage:
Size: 16.6 KB

Statistics

Stars: 0
Watchers: 2
Forks: 0
Open Issues: 0
Releases: 0

Created over 4 years ago · Last pushed about 4 years ago

Metadata Files

Readme License Citation Authors

README.md

Minerva 2 WPRDF Convertor

Get data at https://covid19map.elixir-luxembourg.org/minerva/ under Info, 'source file' as a zip file.

Unzip the content in a newly created data folder. After that, replace spaces in the filenames into underscores:

shell cd data/submaps rename 's/\s/_/g' -- *.xml

Download the BridgeDb mapping file

Download Hs_Derby_Ensembl_91.bridge (or similar) and put it in this folder. Check the file name in the convert.groovy.

Converting Minerva SMBL files

Easiest is just to use the Makefile:

shell make all.ttl

Step by step

Example conversion:

shell groovy convert.groovy data/submaps/Apoptosis\ pathway.xml

The resulting Turtle can be validated with:

shell cat foo.ttl | rapper -i turtle -t -q - . > /dev/null

(Install rapper with apt install raptor2-utils on Debian/Ubuntu.)

Owner

Name: Egon Willighagen
Login: egonw
Kind: user
Location: Maastricht, The Netherlands
Company: @BiGCAT-UM

Website: https://chem-bla-ics.blogspot.com/
Repositories: 530
Profile: https://github.com/egonw

Open scientist teaching and doing research at Maastricht University.

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite the WikiPathways RDF paper, as the RDF output is described in that paper."
authors:
  - family-names: Willighagen
    given-names: Egon
    orcid: https://orcid.org/0000-0001-7542-0286
title: Minerva 2 WPRDF
version: 0.0.1-SNAPSHOT
url: "https://github.com/egonw/minerva2rdf"
preferred-citation:
  type: article
  title: "Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources"
  authors:
  - family-names: Waagmeester
    given-names: Andra
  - family-names: Summer-Kutmon
    given-names: Martina
  - family-names: Riutta
    given-names: Anders
  - family-names: Miller
    given-names: Ryan
  - family-names: Willighagen
    given-names: Egon
  - family-names: Evelo
    given-names: Chris T
  - family-names: Pico
    given-names: Alexander R.
  doi: 10.1371/JOURNAL.PCBI.1004989
  year: 2016
  month: 6
  day: 23
  journal: PLOS Computational Biology
  volume: 12
  issue: 6
  url: https://doi.org/10.1371/JOURNAL.PCBI.1004989

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