Closed ivanerill closed 6 years ago
beckyjackson
commented
6 years ago Thank you for calling our attention to this @ivanerill - there are definitely issues in this node that need to be resolved. We will be working on this as soon as everyone is back from the holidays.
ivanerill
commented
6 years ago Perfect, let me know how I can contribute. Happy holidays!
beckyjackson
commented
6 years ago Hi @ivanerill - I wanted to give you an update on what we've been working on in regards to this issue. Please let me know if you have any suggestions!
We would like to deprecate the class 'array experiment evidence' and move all the children to more appropriate locations. We feel that the classes should be categorized based on what is being analyzed, rather than the technique or technology. This means most of them will be relocated to 'transcript expression evidence'.
As for the microarray evidence types you mentioned above... the naming of microarrays is a bit foggy. Rather than choosing one label that may or may not confuse users, we are proposing to label the microarray classes based on what is being hybridized to what is immobilized on a surface. For example, 'cDNA to DNA expression microarray' involves RNA being reverse transcribed to cDNA, then hybridized to DNA. Any relevant terms will be merged together.
Oligonucleotide arrays can actually be used for DNA, RNA, or protein binding. 'protein-binding microarray evidence' should be moved to 'protein binding evidence', and then 'oligonucleotide microarray evidence' could be included as a related synonym for both 'expression microarray evidence' and 'protein-binding microarray evidence'.
For the other array experiment evidence children... 'CpG island microarray evidence' will be merged into 'differential methylation hybridization evidence' and 'tissue microarray evidence' will be moved to be a child of 'cytochemistry evidence'.
Sorry this response is so long, and hopefully it makes sense. I'm making a draft of the changes in Protege now, so if you'd like to see that file, just let me know.
beckyjackson
commented
6 years ago The changes have been pushed to eco-edit.owl and will be live with our March release. Please let me know if you have any thoughts, otherwise we will close this issue. Thanks! 🙂
ivanerill
commented
6 years ago The changes look good to me. Thanks!
On Thu, Feb 8, 2018 at 9:17 AM, Rebecca Tauber notifications@github.com wrote:
The changes have been pushed to eco-edit.owl and will be live with our March release. Please let me know if you have any thoughts, otherwise we will close this issue. Thanks! 🙂
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ECO now contains many evidence terms for "microarray evidence". On quick inspection, I can see:
I fail to see why this plurality is necessary. I can understand that Affymetrix and Nimblegen are specialized microarray types, and that protein-DNA binding is a different type of evidence from conventional DNA arrays. I don't see, however, how ECO:0005524, ECO:0000104 or ECO:0000097 should be distinct terms. As far as I know, all arrays are based on cDNA strands isolated on a surface, and exploit RNA hybridization (directly or after RT-PCR) on those probes for detection, with the canonical application being measurement of RNA expression levels.