Integrating data of different formats is particularly challenging given the many different layouts of data. This project involved modifying a file that had non-tabular data displayed in a single column. Each term was separated by a [Term] entry, and fields for each term were separated by a colon, see below:
| [Term] |
| id: GO:0000001 |
| name: mitochondrion inheritance |
| namespace: biological_process |
| def: The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton. [GOC:mcc PMID:10873824 PMID:11389764] |
| synonym: mitochondrial inheritance EXACT [] |
| is_a: GO:0048308 ! organelle inheritance |
| is_a: GO:0048311 ! mitochondrion distribution |
| [Term] |
| id: GO:0000002 |
| name: mitochondrial genome maintenance |
| namespace: biological_process |
| def: The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome. [GOC:ai GOC:vw] |
| is_a: GO:0007005 ! mitochondrion organization |
| [Term] |
| id: GO:0000003 |
| name: reproduction |
| namespace: biological_process |
| alt_id: GO:0019952 |
| alt_id: GO:0050876 |
| def: The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. [GOC:go_curators GOC:isa_complete GOC:jl |
| ISBN:0198506732] |
| subset: goslim_agr |
| subset: goslim_chembl |
| subset: goslim_flybase_ribbon |
| subset: goslim_generic |
| subset: goslim_pir |
| subset: goslim_plant |
| synonym: reproductive physiological process EXACT [] |
| xref: Wikipedia:Reproduction |
From above, you can see we have three terms (GO:0000001, GO:0000002, and GO:0000003). However, to join these to another dataset in tabular format we need to process this file into tabular format that appears as this:
| GO | Name | Namespace | alt_id | Def |
|---|---|---|---|---|
| GO:0000001 | mitochondrion inheritance | biological_process | The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton. [GOC:mcc, PMID:10873824, PMID:11389764] | |
| GO:0000002 | mitochondrial genome maintenance | biological_process | The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome. [GOC:ai, GOC:vw] | |
| GO:0000003 | reproduction | biological_process | GO:0019952,GO:0050876 | |
| GO:0000005 | obsolete ribosomal chaperone activity | molecular_function | OBSOLETE. Assists in the correct assembly of ribosomes or ribosomal subunits in vivo, but is not a component of the assembled ribosome when performing its normal biological function. [GOC:jl, PMID:12150913] | |
| GO:0000006 | high-affinity zinc transmembrane transporter activity | molecular_function | Enables the transfer of zinc ions (Zn2+) from one side of a membrane to the other, probably powered by proton motive force. In high-affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations. [TC:2.A.5.1.1] | |
| GO:0000007 | low-affinity zinc ion transmembrane transporter activity | molecular_function | Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Zn2+ = Zn2+, probably powered by proton motive force. In low-affinity transport the transporter is able to bind the solute only if it is present at very high concentrations. [GOC:mtg_transport, ISBN:0815340729] |
To do this, we will run a python script that will search through the file for particular breakpoints, then grab selected fields and store them in a new table.
Additionally, this revised file will be used to make a joins to the annotation file in my data wrangling with tidyr and dplyr repository.
This original file is a gene ontology definition file downloaded from http://geneontology.org/ in OBO format. The annotation file that this will be joined to is already in tabular format, so we need to run a simple script that will do the conversion needed.
Fields pulled from the OBO file include the ID, Name, Namespace, alt_id (these are concatenated into a single column - comma separated), and Def.
The script is the file goconversion.py and needs to be downloaded along with the files in the supporting.files folder. Running the script will create a go.obo.txt file that is tab delimited with the fields indicated above.
Ashburner, et al. (2000, 2000/05/01). Gene Ontology: tool for the unification of biology. Nature Genetics, 25(1), 25-29. https://doi.org/10.1038/75556
Gene Ontology, C. (2021). The Gene Ontology resource: enriching a GOld mine. Nucleic acids research, 49(D1), D325-D334. https://doi.org/10.1093/nar/gkaa1113