PMID:12485443 and others used for lipid metabolism (annotating readouts)

[ValWood]

Reviewing the annotation intersection violations alerted us to:

https://amigo.geneontology.org/amigo/reference/PMID:12485443 This paper describes plasma membrane lipid profiling, and as such isn't suitable to make an annotation to "lipid metabolism". There is no evidence for a role in lipid metabolism, the paper is really only looking at plasma membrane lipid composition.

The assayed gene block1s6 (HSP6) has a role in lysosomal transport, and in the formation of specialized organelles of the endosomal-lysosomal system, such as melanosomes and platelet dense granules. Bloc1s6 appears to be involved in protein sorting from the endosome and the annotations below are indirect (readouts):

Bloc1s6 protein transmembrane transport PMID:28576874 IMP 20231205 Bloc1s6 glutamate metabolic process PMID:28701731 IMP 20231212 Bloc1s6 phospholipid metabolic process PMID:28701731 IMP 20231212 Bloc1s6 glutamine metabolic process PMID:28701731 IMP 20231212 Bloc1s6 gene expression PMID:28701731 IMP 20231212 Bloc1s6 adenosine metabolic process PMID:28701731 IMP 20231212 Bloc1s6 amino acid metabolic process PMID:28701731 IMP 20231212 Bloc1s6 gene expression PMID:30498428 IMP PMID:30498428 IMP 20231212 Bloc1s6 lipid metabolic process PMID:30710063 IMP 20231213 Bloc1s6 multicellular organism growth PMID:19381131 IMP 20231204 Bloc1s6 response to activity PMID:19381131 IMP 20231204 Bloc1s6 gene expression PMID:16439805 IMP 20231129 Bloc1s6 protein targeting PMID:16760431 IMP 20231129 Bloc1s6 bradykinin biosynthetic process PMID:12485443 IMP 20231129 Bloc1s6 intracellular nitric oxide homeostasis PMID:12485443 IMP 20231129 Bloc1s6 ATP metabolic process PMID:12485443 IMP 20231129

These would be OK to make phenotype annotations in your local system, but are not suitable for GO annotation where we are trying to capture the direct roles of gene products.

@LiNiMGI could you assign the ticket to the originating curator, and refer them to the guidelines for making GO annotations using the IMP evidence code and annotating phenotypes: https://wiki.geneontology.org/Annotating_from_phenotypes and the book chapter written by Sylvainand Pascale in the GO handbook I also find very useful https://link.springer.com/protocol/10.1007/978-1-4939-3743-1_4 particularly section 2.4.3 Phenotypes

Please let us know if you have any concerns

CC @pgaudet