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related-sciences / ensembl-genes

Extract the Ensembl genes catalog to simple tables
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add support for rat species #6

Closed dhimmel closed 3 years ago

dhimmel commented 3 years ago

refs https://github.com/related-sciences/ensembl-genes/issues/4

dhimmel commented 3 years ago

Here's output readme for rat from a local export. @ACastanza does this look okay, besides the mhc column?

# Output ## Release info - release: 104 - source commit: `1d7dbadc69d52e303d6d0403f4d8c430879c8f4c ` - created in action: ## Table heads The first 10 rows of each exported table is shown below. ### genes Primary table of ensembl genes with IDs, symbols, and genomic location information. Most users will want to filter this dataset to representative genes only, via the `is_representative_gene` column. | ensembl_gene_id | ensembl_gene_version | gene_symbol | gene_symbol_source_db | gene_symbol_source | gene_biotype | gene_description | ensembl_source | ensembl_created_date | ensembl_modified_date | coord_system_version | coord_system | chromosome | seq_region_exc_type | seq_region | seq_region_start | seq_region_end | seq_region_strand | primary_assembly | lrg_gene_id | mhc | ensembl_representative_gene_id | |:-------------------|-----------------------:|:---------------|:-------------------------|:---------------------|:---------------|:------------------------------------------------------------------------------|:-----------------|:-----------------------|:------------------------|:-----------------------|:---------------|-------------:|:----------------------|-------------:|-------------------:|-----------------:|--------------------:|:-------------------|:--------------|:------|:---------------------------------| | ENSRNOG00000000001 | 5 | AABR07013255.1 | Clone_based_ensembl_gene | AABR07013255.1 | pseudogene | | ensembl | 2009-07-29 15:36:02 | 2015-04-02 16:53:59 | Rnor_6.0 | chromosome | 2 | | 2 | 230660664 | 230662084 | 1 | True | | no | ENSRNOG00000000001 | | ENSRNOG00000000007 | 7 | Gad1 | RGD | 2652 | protein_coding | glutamate decarboxylase 1 [Source:RGD Symbol;Acc:2652] | ensembl | 2009-07-29 15:36:02 | 2015-04-02 16:53:59 | Rnor_6.0 | chromosome | 3 | | 3 | 56861396 | 56902157 | 1 | True | | no | ENSRNOG00000000007 | | ENSRNOG00000000008 | 7 | Alx4 | RGD | 1310201 | protein_coding | ALX homeobox 4 [Source:RGD Symbol;Acc:1310201] | ensembl | 2009-07-29 15:36:02 | 2015-04-02 16:53:59 | Rnor_6.0 | chromosome | 3 | | 3 | 82548959 | 82585531 | 1 | True | | no | ENSRNOG00000000008 | | ENSRNOG00000000009 | 5 | Tmco5b | RGD | 1561237 | protein_coding | transmembrane and coiled-coil domains 5B [Source:RGD Symbol;Acc:1561237] | ensembl | 2009-07-29 15:36:02 | 2015-04-02 16:53:59 | Rnor_6.0 | chromosome | 3 | | 3 | 104749051 | 104765436 | 1 | True | | no | ENSRNOG00000000009 | | ENSRNOG00000000010 | 5 | Cbln1 | RGD | 1562813 | protein_coding | cerebellin 1 precursor [Source:RGD Symbol;Acc:1562813] | ensembl | 2009-07-29 15:36:02 | 2009-07-29 15:36:02 | Rnor_6.0 | chromosome | 19 | | 19 | 20607507 | 20611316 | 1 | True | | no | ENSRNOG00000000010 | | ENSRNOG00000000012 | 5 | Tcf15 | RGD | 1308464 | protein_coding | transcription factor 15 [Source:RGD Symbol;Acc:1308464] | ensembl | 2009-07-29 15:36:02 | 2012-11-09 06:35:19 | Rnor_6.0 | chromosome | 3 | | 3 | 147643250 | 147649504 | 1 | True | | no | ENSRNOG00000000012 | | ENSRNOG00000000017 | 7 | Steap1 | RGD | 1311543 | protein_coding | STEAP family member 1 [Source:RGD Symbol;Acc:1311543] | ensembl | 2009-07-29 15:36:02 | 2015-04-02 16:53:59 | Rnor_6.0 | chromosome | 4 | | 4 | 25435873 | 25446461 | 1 | True | | no | ENSRNOG00000000017 | | ENSRNOG00000000021 | 3 | AABR07061902.1 | Clone_based_ensembl_gene | AABR07061902.1 | pseudogene | | ensembl | 2009-07-29 15:36:02 | 2012-11-09 06:35:19 | Rnor_6.0 | chromosome | 4 | | 4 | 151987078 | 151988279 | 1 | True | | no | ENSRNOG00000000021 | | ENSRNOG00000000024 | 7 | Hebp1 | RGD | 1304581 | protein_coding | heme binding protein 1 [Source:RGD Symbol;Acc:1304581] | ensembl | 2009-07-29 15:36:02 | 2015-04-02 16:53:59 | Rnor_6.0 | chromosome | 4 | | 4 | 168903565 | 168933079 | -1 | True | | no | ENSRNOG00000000024 | | ENSRNOG00000000033 | 5 | Tmcc2 | RGD | 1311960 | protein_coding | transmembrane and coiled-coil domain family 2 [Source:RGD Symbol;Acc:1311960] | ensembl | 2009-07-29 15:36:02 | 2015-04-02 16:53:59 | Rnor_6.0 | chromosome | 13 | | 13 | 49132667 | 49169918 | -1 | True | | no | ENSRNOG00000000033 | ### alt_alleles This is an intermediate table that groups genes if they are alternate alleles of eachother. A representative gene is selected from each group. | ensembl_gene_id | alt_allele_group_id | alt_allele_is_representative | primary_assembly | seq_region | alt_allele_attrib | ensembl_created_date | ensembl_representative_gene_id | is_representative_gene | representative_gene_method | |-------------------|-----------------------|--------------------------------|--------------------|--------------|---------------------|------------------------|----------------------------------|--------------------------|------------------------------| ### old_to_newest This table maps outdated gene symbols to their newest gene symbol, traversing multiple levels of replacement if necessary. When `is_current` is False, then the newest replacement is not a current gene. | old_ensembl_gene_id | newest_ensembl_gene_id | is_current | |:----------------------|:-------------------------|:-------------| | ENSRNOG00000000132 | ENSRNOG00000031425 | True | | ENSRNOG00000000194 | ENSRNOG00000031589 | False | | ENSRNOG00000000194 | ENSRNOG00000045932 | True | | ENSRNOG00000000194 | ENSRNOG00000045940 | True | | ENSRNOG00000000194 | ENSRNOG00000046072 | True | | ENSRNOG00000000194 | ENSRNOG00000046182 | True | | ENSRNOG00000000194 | ENSRNOG00000046425 | True | | ENSRNOG00000000194 | ENSRNOG00000047636 | True | | ENSRNOG00000000194 | ENSRNOG00000047749 | True | | ENSRNOG00000000194 | ENSRNOG00000048331 | True | ### updates This dataset updates ensembl genes to current, representative ensembl genes. We refer to it as the 'omni-updater'. When ingesting external datasets that use Ensembl gene IDs, we recommend joining with this table. Current, representative genes map to themselves. | input_ensembl_gene_id | ensembl_gene_id | input_current | input_representative | input_maps_to_n_genes | n_inputs_map_to_gene | |:------------------------|:-------------------|:----------------|:-----------------------|------------------------:|-----------------------:| | ENSRNOG00000000001 | ENSRNOG00000000001 | True | True | 1 | 1 | | ENSRNOG00000000007 | ENSRNOG00000000007 | True | True | 1 | 1 | | ENSRNOG00000000008 | ENSRNOG00000000008 | True | True | 1 | 1 | | ENSRNOG00000000009 | ENSRNOG00000000009 | True | True | 1 | 1 | | ENSRNOG00000000010 | ENSRNOG00000000010 | True | True | 1 | 1 | | ENSRNOG00000000012 | ENSRNOG00000000012 | True | True | 1 | 1 | | ENSRNOG00000000017 | ENSRNOG00000000017 | True | True | 1 | 1 | | ENSRNOG00000000021 | ENSRNOG00000000021 | True | True | 1 | 1 | | ENSRNOG00000000024 | ENSRNOG00000000024 | True | True | 1 | 1 | | ENSRNOG00000000033 | ENSRNOG00000000033 | True | True | 1 | 1 | ### xrefs This dataset contains cross-references (xrefs) from Ensembl genes to various external gene resources. | ensembl_gene_id | xref_source | xref_accession | xref_label | xref_description | xref_info_type | xref_linkage_annotation | |:-------------------|:-------------------------|:-------------------|:-------------------|:--------------------------------------------------|:-----------------|:--------------------------| | ENSRNOG00000000001 | ArrayExpress | ENSRNOG00000000001 | ENSRNOG00000000001 | | DIRECT | | | ENSRNOG00000000001 | Clone_based_ensembl_gene | AABR07013255.1 | AABR07013255.1 | | MISC | | | ENSRNOG00000000007 | ArrayExpress | ENSRNOG00000000007 | ENSRNOG00000000007 | | DIRECT | | | ENSRNOG00000000007 | EntrezGene | 24379 | Gad1 | glutamate decarboxylase 1 | DEPENDENT | | | ENSRNOG00000000007 | Reactome_gene | R-RNO-112310 | R-RNO-112310 | Neurotransmitter release cycle | DIRECT | | | ENSRNOG00000000007 | Reactome_gene | R-RNO-112315 | R-RNO-112315 | Transmission across Chemical Synapses | DIRECT | | | ENSRNOG00000000007 | Reactome_gene | R-RNO-112316 | R-RNO-112316 | Neuronal System | DIRECT | | | ENSRNOG00000000007 | Reactome_gene | R-RNO-888568 | R-RNO-888568 | GABA synthesis | DIRECT | | | ENSRNOG00000000007 | Reactome_gene | R-RNO-888590 | R-RNO-888590 | GABA synthesis, release, reuptake and degradation | DIRECT | | | ENSRNOG00000000007 | RGD | 2652 | Gad1 | glutamate decarboxylase 1 | DIRECT | | ### xref_ncbigene This dataset contains cross-references (xrefs) from Ensembl genes to NCBI (Entrez) genes. | ensembl_representative_gene_id | ncbigene_id | |:---------------------------------|--------------:| | ENSRNOG00000000007 | 24379 | | ENSRNOG00000000008 | 296511 | | ENSRNOG00000000009 | 366158 | | ENSRNOG00000000010 | 498922 | | ENSRNOG00000000012 | 296272 | | ENSRNOG00000000017 | 297738 | | ENSRNOG00000000024 | 362454 | | ENSRNOG00000000033 | 305095 | | ENSRNOG00000000034 | 289419 | | ENSRNOG00000000035 | 689712 | ### xref_go This dataset contains cross-references (xrefs) from Ensembl genes to Gene Ontology terms, as asserted by Gene Ontology annotations. | ensembl_gene_id | go_id | go_label | go_evidence_codes | xref_info_types | ensembl_transcript_ids | ensembl_representative_gene_id | |:-------------------|:-----------|:---------------------------------------------|:--------------------|:------------------|:----------------------------------------------------------------------------|:---------------------------------| | ENSRNOG00000000007 | GO:0003824 | catalytic activity | IEA | DEPENDENT,DIRECT | ENSRNOT00000000008,ENSRNOT00000087134,ENSRNOT00000087712 | ENSRNOG00000000007 | | ENSRNOG00000000007 | GO:0004351 | glutamate decarboxylase activity | IEA,ISO,ISS | PROJECTION,DIRECT | ENSRNOT00000000008,ENSRNOT00000084375,ENSRNOT00000087712 | ENSRNOG00000000007 | | ENSRNOG00000000007 | GO:0005737 | cytoplasm | IEA,ISO | PROJECTION,DIRECT | ENSRNOT00000000008,ENSRNOT00000087712 | ENSRNOG00000000007 | | ENSRNOG00000000007 | GO:0005938 | cell cortex | IEA,ISO | PROJECTION,DIRECT | ENSRNOT00000000008,ENSRNOT00000087712 | ENSRNOG00000000007 | | ENSRNOG00000000007 | GO:0009449 | gamma-aminobutyric acid biosynthetic process | IDA | DIRECT | ENSRNOT00000000008,ENSRNOT00000087712 | ENSRNOG00000000007 | | ENSRNOG00000000007 | GO:0016595 | glutamate binding | IDA | DIRECT | ENSRNOT00000000008,ENSRNOT00000087712 | ENSRNOG00000000007 | | ENSRNOG00000000007 | GO:0016829 | lyase activity | IEA | DIRECT | ENSRNOT00000000008,ENSRNOT00000084375,ENSRNOT00000087134,ENSRNOT00000087712 | ENSRNOG00000000007 | | ENSRNOG00000000007 | GO:0016831 | carboxy-lyase activity | IEA | DEPENDENT,DIRECT | ENSRNOT00000000008,ENSRNOT00000084375,ENSRNOT00000087134,ENSRNOT00000087712 | ENSRNOG00000000007 | | ENSRNOG00000000007 | GO:0019752 | carboxylic acid metabolic process | IEA | DEPENDENT,DIRECT | ENSRNOT00000000008,ENSRNOT00000084375,ENSRNOT00000087134,ENSRNOT00000087712 | ENSRNOG00000000007 | | ENSRNOG00000000007 | GO:0030170 | pyridoxal phosphate binding | IDA,IEA | DEPENDENT,DIRECT | ENSRNOT00000000008,ENSRNOT00000084375,ENSRNOT00000087134,ENSRNOT00000087712 | ENSRNOG00000000007 |
ACastanza commented 3 years ago

This looks pretty good. I also really like the omni-updater, tracking old ensembl ids was something I'd always intended to get to but was difficult data to get to.