bio explain: show definitions
We implemented the
bio explain command to facilitate the quick explorations of the Gene and Sequence Ontologies.
For more information on ontologies, consult The Biostar Handbook chapter Sequence and Gene Ontology: What do the words mean?. To install
pip install bio --upgrade bio --download
The full documentation for
bio is maintained at https://www.bioinfo.help/.
Prints the contents of the database:
# Content: 43,878 gene ontology terms; 2,354 sequence ontology terms
As we can see the database currently contains
43,878 gene ontology and
2,354 sequence ontology terms.
Explain a term
bio explain exon
prints that the term is part of the Sequence Ontology (SO) with number
SO:0000147 and is defined as:
## exon (SO:0000147) A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. Parents: - transcript_region Children: - coding_exon - noncoding_exon - interior_exon - decayed_exon (non_functional_homolog_of) - pseudogenic_exon (non_functional_homolog_of) - exon_region (part_of) - exon_of_single_exon_gene
You can now query the parent or child relationships:
bio explain transcript_region
bio explain coding_exon
Explain term by identifier
If you know the identifier then you may use it directly
bio explain SO:0000147 or
bio explain GO:2000147
Explain more complex terms
All words have to match exactly; thus, try simpler terms before going full length.
bio explain regulation bio explain positive regulation bio explain positive regulation of x bio explain positive regulation of xanthophore differentiation
What is xantophore?
bio explain xanthophore
## xanthophore (GO:0031633) A chromatophore containing yellow pigment. Parents: - plasma membrane-derived chromatophore
Showing the term lineage
bio explain exon --lineage
SO:0000110 sequence_feature SO:0000001 region SO:0001411 biological_region SO:0000833 transcript_region ## exon (SO:0000147) A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. Children: - coding_exon - noncoding_exon - interior_exon - decayed_exon (non_functional_homolog_of) - pseudogenic_exon (non_functional_homolog_of) - exon_region (part_of) - exon_of_single_exon_gene
Searching the database
Any query that is not matched will be searched for. The
-go flag restricts tje search for gene ontology while
-so restricts the search for sequence ontology. To search for both sequence and gene ontology:
# Searces both ontologies bio explain histone | head # Search gene ontology only bio explain histone --go | head # Search gene ontology only bio explain histone --so |head
Build the newest version locally
You may build a database with the newest data:
bio explain --build
The command will download the most up-to-date ontology data and build a new database. The process might take about half an hour - through the completion speed depends on the hard drive write speed, solid-state drives finish much faster.