Closed khanspers closed 6 years ago
Another related issue (renamed this ticket): The gmt files for some species don't match contents of corresponding gpml dir. For example, At gmt file lists 18 pathways, but the gpml dir has 26 pathways. Also observed in other species (Hs, Os, Ce...).
I'll check when I am back at work but it only includes pathways that have at least one identifier that can be mapped to entrez gene. If the pathway doesn't have any identifier that maps to entrez gene then the pathway is not added. That is probably the reason why the numbers don't match. Species for which gene identifiers are not available in entrez gene, no gmt file is created.
On Wed, Jul 18, 2018, 20:11 Kristina Hanspers notifications@github.com wrote:
Another related issue (renamed this ticket): The gmt files for some species don't match contents of corresponding gpml dir. For example, At gmt file lists 18 pathways, but the gpml dir has 26 pathways. Also observed in other species (Hs, Os, Ce...).
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Right, I checked and this is the reason for both of these issues. Closing.
The gmt folder of downloads only contains gmt files for 17 of the 25 species in the Analysis Collection. Missing species:
Solanum lycopersicum Hordeum vulgare Zea mays Gibberella Zeae Bacillus subtilis E.coli Mycobacterium tuberculosis Plasmodium falciparum