Data dumps for B. tabaci Uganda-1 directs to 404 error

Alignment of External Feature – unable to retrieve sequence from Uniprot/SwissProt

This is the link to the page ([https://dec2021.archive.ensembl.org/Homo_sapiens/Transcript/Similarity/Align?db=core;extdb=uniprot/swissprot;g=ENSG00000100345;r=22:36281280-36388010;sequence=P35579.240;t=ENST00000216181])

The URL incorrectly contains the UniProt entry and its version (P35579.240), and this leads to the problem.

E.g https://dec2021.archive.ensembl.org/Homo_sapiens/Transcript/Similarity/Align?db=core;extdb=uniprot/swissprot;g=ENSG00000100345;r=22:36281280-36388010;sequence=P35579.240;t=ENST00000216181

becomes

https://dec2021.archive.ensembl.org/Homo_sapiens/Transcript/Similarity/Align?db=core;extdb=uniprot/swissprot;g=ENSG00000100345;r=22:36281280-36388010;sequence=P35579;t=ENST00000216181

Missing Protein Features for Beta Vulgaris in Plants BioMart

Duplicate species in protists and fungi

So we already have an older version in protists (version 1). To keep with how we have thought about this in Ensembl, it may be sensible to only have this species in protists.

Data dumps, compara, search indices etc has made this really complex. Temporarily, the species has gone off Ensembl Protists. This will be reinstated in release 107. Until then, please use our archive sites for this data. Meanwhile, there is a newer version in Ensembl Fungi. We will remove this in release 108. After that point, this species will go back to existing only in Ensembl Protists.

Missing alias in meta table for Rat

Specifically, the record with meta.meta_key = ‘species.alias’ are the missing ones.

As a result, the Perl API (Registry) can query the DB using the “species.production_name” only, which is “Rattus_norvegicus”.
Also, this must be an exact string match.

Although not blocking an issue, it was customary to use aliases – e.g. “Rat”, “Rattus norvegicus” – to query the DB.

In the rat case, the string is “rattus_norvegicus” (without quotes).

UniProt Variants track out of date

The track will be updated in our next release, 107

Broken Cactus HAL alignment on the web for Brugia malayi

The issue does not affect the whole _Brugia malayi_ genome. There are regions in _Brugia malayi_ for which the display works.

Missing Gene names attributes in Zea_mays GTF/GFF Files

Arabidopsis names have ” in their symbol

Gene: B”BETA (AT5G28850)[https://plants.ensembl.org/Arabidopsis_thaliana/Gene/Summary?g=AT5G28850;r=5:10876788-10881485;t=AT5G28850.1;db=core]

Gene: U2B” (AT2G30260) [https://plants.ensembl.org/Arabidopsis_thaliana/Gene/Summary?g=AT2G30260;r=2:12905345-12907665;t=AT2G30260.1;db=core]

which causes issues with searching for these gene symbols.

Missing Pig microarray data

Corrupted conservation scores in Compara MySQL dump file

This corruption was identified during the course of Compara MySQL data dumps, and the Compara release database ‘conservation_score’ table was restored from a backup containing the correct data.

However, the fix was not applied to the conservation-score MySQL dump file at the following location:

https://ftp.ensembl.org/pub/release-106/mysql/ensembl_compara_106/conservation_score.txt.gz

As a result, while a query against ‘ensembl_compara_106’ on the Ensembl public MySQL server will return correct conservation-score data, the same query applied to a locally installed ‘ensembl_compara_106’ database may encounter an error or return invalid conservation-score data.

Because the issue was fixed in the ‘ensembl_compara_106’ release database, it will not affect Ensembl Compara 107 or later.

Unfortunately, there is no equivalent workaround for the ‘fish’ species set, because its alignment and associated conservation scores were updated in Ensembl 106. It is safe to have the Ensembl 105 fish conservation scores in a Compara 106 database, as their database IDs don’t overlap with those of the Ensembl 106 fish alignments. But they will be taking up space in the ‘conservation_score’ table. If this is a problem, the 105 fish conservation scores can be removed by deleting rows from the ‘conservation_score’ table where they have a ‘genomic_align_block_id’ between 19720000000001 and 19729999999999 (inclusive).

Malfunctioning search for Hyaloperonospora arabidopsidis in 106

Description: Users may find that doing a search for Hyaloperonospora arabidopsidis on our sites returns it as a Fungi. However, please note that this species has now being placed back in Ensembl Protists. The link to this species in Ensembl Protists is: (http://protists.ensembl.org/Hyaloperonospora_arabidopsidis)