Fission_yeast_annotation

[dbitton]

go to http://www.pombase.org/downloads/data-mappings

first file tab delimited file of systematic name, primary name (empty if not assigned), followed by all synonyms wget ftp://ftp.ebi.ac.uk/pub/databases/pombase/pombe/Mappings/allNames.tsv

tab delimited file of systematic identifier mapped to UniProt Accession Number wget ftp://ftp.ebi.ac.uk/pub/databases/pombase/pombe/Mappings/PomBase2UniProt.tsv

systematic name, primary name (empty if not assigned), synonyms (empty if not assigned), followed by gene product description wget ftp://ftp.ebi.ac.uk/pub/databases/pombase/pombe/Mappings/sysID2product.tsv

Create the following table

• Systematic Name (primary name)
• EC number (blank)
• PombePD (description)
• Our_annotation (blank)
• Phenotype (blank)
• Function (blank)
• Keywords (blank)
• PubMedID (systematic id)
• GeneDB (description)
• Remarks (blank)
• Swissprot (uniprotid)
• Type (blank)
• DBid (blank)
• GO biological process (blank)
• GO molecular function (blank)
• GO cellular component (blank)
• RefSeq (blank)
• UniGene (blank)

first read allnames.tsv guided by sytematic ID rather than names (5416...) then fill in the table accordingly, description (sysID2product.tsv),,,,, PubmedID (primary names allnames.tsv column 2), GeneDB (description sysID2product.tsv), uniprot (PomBase2UniProt.tsv, column)

[dbitton]

pompep wget ftp://ftp.ebi.ac.uk/pub/databases/pombase/FASTA/pep.fa.gz

[sinanshi]

Note, the number of rows should always be the same.

[sinanshi]

SGD_features.tab from http://downloads.yeastgenome.org/curation/chromosomal_feature/SGD_features.tab. non empty number of rows - 5416

ftp://ftp.ebi.ac.uk/pub/databases/pombase/pombe/Mappings/allNames.tsv non empty number of rows - 4508

Intersection between these two files -- 2021

[sinanshi]

• PubMedID (systematic id)
• sysID2product.tsv systematic name, primary name (empty if not assigned), synonyms (empty if not assigned), followed by gene product description

Do you mean systematic_id by primary name?

[sinanshi]

modification:

guided by uniport id use primary name , while primary name doesn't exsit fill in systematic id

[sinanshi]

5139 rows

[sinanshi]

Neither primary name nor systematic name in all_name.tsv is not unique (2 duplication). Remove all the non-unique entry.

[sinanshi]

work done, please check later.

[dbitton]

great, all the update?

[dbitton]

I am aware of the two duplicates

[sinanshi]

No, only the Fission_yeast_annotation.txt. There are two duplicates in both primaray and systematic names.