A bot that updates Wikidata with information from the Complex Portal
Data from http://ftp.ebi.ac.uk/pub/databases/intact/complex/current/complextab/.
Usage: python3 update_complex.py -s [species id] -w [boolean]
Arguments:
--species/-s : a species NCBI ID
--wikidata/-w : 1 to add new complex to Wikidata, 0 to also update the existing ones.
--number/-n: The number of complexes to add to Wikidata.
Currently, errors are added to the errors/log folder.
To run for all species, run:
python3 src/update_all_complexes.py -w 0 -n 99999
To know the current species covered by Complex Portal, run
python3 check_ids.py .
You should get a table similar to the one below:
| itemLabel | id | |
|---|---|---|
| 0 | house mouse | 10090 |
| 1 | Marbled electric ray | 7788 |
| 2 | Oryctolagus cuniculus | 9986 |
| 3 | Red Junglefowl | 9031 |
| 4 | Escherichia coli | 562 |
| 5 | Tetronarce californica | 7787 |
| 6 | Caenorhabditis elegans | 6239 |
| 7 | Drosophila melanogaster | 7227 |
| 8 | Ovis aries | 9940 |
| 9 | Arabidopsis thaliana | 3702 |
| 10 | Lymnaea stagnalis | 6523 |
| 11 | Homo sapiens | 9606 |
| 12 | Canis lupus familiaris | 9615 |
| 13 | African clawed frog | 8355 |
| 14 | Danio rerio | 7955 |
| 15 | Bos taurus | 9913 |
| 16 | wild boar | 9823 |
| 17 | brown rat | 10116 |
| 18 | Escherichia coli K-12 | 83333 |
| 19 | SARSr-CoV | 694009 |
| 20 | Pseudomonas aeruginosa PAO1 | 208964 |
| 21 | Schizosaccharomyces pombe 972h- | 284812 |
| 22 | Saccharomyces cerevisiae S288c | 559292 |
| 23 | SARS-CoV-2 | 2697049 |
- Tiago Lubiana (@lubianat)
- Birgit Meldal
- Egon Willighagen
- Andra Waagmesster
- João Vitor Ferreira ((@jvfe)
(README updated in 15/01/2021)