[Linux] Ontology (3) - bio explain

이전 한 포스팅에서 bio 패키지의 bio fetch와 bio search에 대해 다룬 적이 있다.

bio fetch와 bio search

 

이번 포스팅에서는 SO와 GO를 빠르게 검색해 볼 수 있는 bio explain에 대해 간략히 소개하고자 한다.

 

1. 개념/용어로 찾기

$ bio explain exon

## 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

 

2. ID로 찾기

$ bio explain SO:0000147

## 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

 

3. term lineage 나타내기

$ 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

 

4. 데이터베이스 탐색

 

(1) SO와 GO 데이터베이스 둘 다 포함

$ bio explain histone | head
GO:0000118  histone deacetylase complex
GO:0000123  histone acetyltransferase complex
GO:0000412  histone peptidyl-prolyl isomerization
GO:0000414  regulation of histone h3-k36 methylation
GO:0000415  negative regulation of histone h3-k36 methylation
GO:0000416  positive regulation of histone h3-k36 methylation
GO:0001207  histone displacement
GO:0001208  histone h2a-h2b dimer displacement
GO:0004402  histone acetyltransferase activity
GO:0004407  histone deacetylase activity

 

(2) SO만

$ bio explain histone --so | head
SO:0001221  silenced_by_histone_modification
SO:0001222  silenced_by_histone_methylation
SO:0001223  silenced_by_histone_deacetylation
SO:0001225  gene_silenced_by_histone_modification
SO:0001226  gene_silenced_by_histone_methylation
SO:0001227  gene_silenced_by_histone_deacetylation
SO:0001383  histone_binding_site
SO:0001700  histone_modification
SO:0001701  histone_methylation_site
SO:0001702  histone_acetylation_site

 

(3) GO만

$ bio explain histone --go | head
GO:0000118  histone deacetylase complex
GO:0000123  histone acetyltransferase complex
GO:0000412  histone peptidyl-prolyl isomerization
GO:0000414  regulation of histone h3-k36 methylation
GO:0000415  negative regulation of histone h3-k36 methylation
GO:0000416  positive regulation of histone h3-k36 methylation
GO:0001207  histone displacement
GO:0001208  histone h2a-h2b dimer displacement
GO:0004402  histone acetyltransferase activity
GO:0004407  histone deacetylase activity

---

Reference

The Biostar Handbook: 2nd Edition - István Albert