Change metadata to improve text on annotation downloads page

[kltm]

Currently, a products download page is produced directly from the pipeline and left places like: http://snapshot.geneontology.org/products/pages/downloads.html Some of the text is hard to read for intended audience.

Started by @pgaudet , see: https://github.com/geneontology/go-site/pull/1012 https://github.com/geneontology/go-site/pull/1011

[kltm]

Assuming submitter should match shorthand in groups.yaml I'm surprised that entity_type is uncontrolled. According to @dougli1sqrd none of these are currently used internally, so having them be labels would not be a problem. @cmungall would you know if these fields are used by others?

[cmungall]

I decree we should use biolink model types for entity type.

E.g. https://w3id.org/biolink/vocab/ProteinIsoform

Just use the fragment, e.g. ProteinIsoform. When we get around to adding a json-ld context we will can make the base for the type field be https://w3id.org/biolink/vocab/

Re isoforms, see https://github.com/biolink/biolink-model/issues/230

[suzialeksander]

OK, looks like i just made some changes for https://github.com/geneontology/go-site/issues/847 to change a blank entity type to 'protein', which is an existing type- I think this is an allowed entry?

For the other downloads, the entities they include are:

• TAIR: antisense_RNA, gene_product, lnc_RNA, miRNA, protein, pseudogene, RNA, rRNA, snoRNA, snRNA, transposable_element_gene, tRNA
• WB : gene, protein
• Zfin: protein_coding_gene pseudogene miRNA tRNA protein gene_product
• Dicty: protein snoRNA snRNA gene_product tRNA scRNA RNase_P_RNA RNase_MRP_RNA
• FB: gene_product protein rRNA ncRNA miRNA tRNA snoRNA snRNA
• CGD: gene_product protein
• Ecoli: protein
• Pfalc: mRNA tRNA gene_product ncRNA
• Lmajor: mRNA gene_product (note: only 44x gene product)
• Tbrucei: mRNA gene_product snoRNA tRNA
• MGI: protein_coding_gene pseudogene gene_product gene_segment tRNA_gene scRNA_gene lncRNA_gene protein biological region snRNA_gene miRNA_gene ncRNA_gene snoRNA_gene lincRNA_gene sense_intronic_ncRNA_gene gene rRNA_gene RNase_P_RNA_gene telomerase_RNA_gene mRNA sense_overlap_ncRNA_gene RNase_MRP_RNA_gene SRP_RNA_gene
• Pseudo: protein, tmRNA, ncRNA
• RGD: gene, protein
• SGD: protein gene protein_complex snoRNA tRNA ncRNA rRNA snRNA telomerase_RNA
• Sjap: protein
• Pombe: protein, tRNA, gene_product, snoRNA, rRNA, snRNA, protein_coding_gene
• Xenbase: protein, gene

@pgaudet what do we want to label these as?

[pgaudet]

@suzialeksander Let's talk about his tomorrow?

[pgaudet]

Decision is to remove this column completely. The goal is to provide species-specific files containing all types of entities.

[suzialeksander]

entity type and submitter are not columns in the New Downloads Table.