add support for rat species

[dhimmel]

refs #4

[dhimmel]

@ACastanza do you happen to know the MHC/ xMHC boundaries for rats?

[ACastanza]

I'm not, sorry. I did find this publication: https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC383307/ but it's pretty old and almost certainly doesn't correspond to the current genome assembly which is Rnor_6.0.
Speaking of which, the mouse coordinates will need to be taken from GRCm39.

[dhimmel]

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: https://github.com/None/actions/runs/None

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]

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.