https://github.com/applicativesystem/candida-ontology-network

analyzing candida ontology terms for network analysis
https://github.com/applicativesystem/candida-ontology-network

bioinformatics genome-analysis genome-anntoation network network-analysis ontology ontology-alignment ontology-search

Last synced: 7 days ago
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analyzing candida ontology terms for network analysis

• Host: GitHub
• URL: https://github.com/applicativesystem/candida-ontology-network
• Owner: applicativesystem
• License: mit
• Created: 2024-08-21T18:05:49.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-08-21T19:08:59.000Z (4 months ago)
• Last Synced: 2024-11-10T20:18:04.737Z (about 1 month ago)
• Topics: bioinformatics, genome-analysis, genome-anntoation, network, network-analysis, ontology, ontology-alignment, ontology-search
• Language: Python
• Homepage:
• Size: 23.4 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# ontoloty-network-candida

- i coded this a faster implementation of the gene ontology analyzer for the candida genomes, given the candida go ontology files and a search GO term, it extracts all the alt_id,  relationship_ids and associated function with those  gene ontology for the network analysis and to link with  the expression analysis.

- This is a test ontology term, you can use any ontology term that you are interested in for making your expression networks.

- The reason, why i coded this, is that if i look at the candida genome database, i was not able to find the associated gene ontologies associated with a specific ontology that i can plot along with the expression into a directed acyclic graph, so i coded this and given an ontology term and the gene ontology file, it will give you all the associated IDs as well as the function.

- The ids can be directly used as a iterable in the network analysis to plot along with the expression as edges and nodes.

```

candidaGORelationAnalyzer("/Users/gauravsablok/Desktop/CodeCheck/broad/goslim_candida.obo",

                         go_search="GO:0042493")

['GO:0042493',

 'alt_id: GO:0017035',

 'GO:0042493',

 'is_a: GO:0042221 | response to chemical']

```

Gaurav Sablok \

University of Potsdam \

Potsdam,Germany