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 bio use:

pip install bio --upgrade
bio --download

The full documentation for bio is maintained at https://www.bioinfo.help/.

Database information

bio explain

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

or

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

prints:

## xanthophore (GO:0031633)

A chromatophore containing yellow pigment.

Parents:
- plasma membrane-derived chromatophore

Showing the term lineage

bio explain exon --lineage

prints:

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.