Flag for automatically filtering out is_suppressed in children?

[Norlock]

I wonder if it's possible to include this feature? There are some huge responses where only 1% is interesting because the rest is just "is_suppressing": true. I also want to make this feature, but I don't know which repo I need to look at. If its really old I will skip the implementation.

[snacktavish]

Hi @Norlock - This possible is in some calls! What call are you using? Can you clarify the behavior you are looking for?

[Norlock]

Yes I'm a software engineer so I'm lacking domain knowledge, I learned that the phylogenetic tree is superior to the taxonomic tree (so I already switched to this one: https://github.com/OpenTreeOfLife/germinator/wiki/Synthetic-tree-API-v3). I'm currently making a connector that will feed that data in to my web app which will display this tree.

My question was related to the /taxonomy/taxon_info endpoint which on the domain bacteria is huge (I already switched to /tree_of_life/node_info). The node_info endpoint is also missing some fields I thought were important data in phylogeny (million years ago, extinct status, or the flags which are included in the taxon_info endpont). Is there a way I can fetch these fields, or is that always included in one of the linked sources?

One more question, can I always trust the taxonomic rank is added to the node (most important species). So I can make a judgement call on what node is interesting for the end user. OneZoom for example knows what groups / clades are interesting. Maybe if you have another suggestion on how to find out which clade is interesting for common people please let me know.

[Norlock]

Ok I just found out, that changing the format to arguson (looks like normal json to me, thank god) has a completely different response body. Its not just the format but also the data, that seems much more useful. I think you have to update the DOCS because I never heard of arguson before and wrote a Newick parser in the mean time...

[snacktavish]

Ah yes - Arguson is our internal translation to JSON and it has a ton more info. Unfortunately, the more common phylogenetic file formats are much more limited. Some more infomation about the Nexson format is here https://github.com/OpenTreeOfLife/phylesystem-api/wiki/NexSON - this is what we use for our input studies. Arguson is a little more complex as it also contains information about the synthesis process.

[Norlock]

Ok are you also using the phylesystem internally for this? Or the synthetic tree, I have ran the importer for the synthetic tree and now some results are missing, I tried looking for 'tyrannosaurus rex' for example. Also the fields seems to be incorrect at times, like I can see some dinosaurs that aren't extinct, or taxon ranks that don't make sense in some rows.

https://evo-splittable.com/display/1_3/10_175/10_916/10_1148/10_3722/10_5189/10_6601/10_7533/10_10104/10_13400/10_16504/10_29331/10_37405/10_51679/10_67572/10_83439/10_99100/10_125082/10_147444/10_191145/10_255716/10_288079/10_322701/10_356769/10_390599/10_448224/10_509446/10_563393/10_617063/10_677522/10_725504/10_768965/10_820449/10

This is the demo-app I'm making so its still a work in progress (you can press / for search to see if something is missing). Do you mind if I have questions I can send you an email? So I don't misuse the GitHub issues for this. Anyway thanks for all the help!

[mtholder]

Hi! The arguson is produced by the tool that serves the https://github.com/OpenTreeOfLife/germinator/wiki/Synthetic-tree-API-v3 services.
Incomplete flagging of extinct taxa has been an issue for a while. We are hoping to move to the CoL-XR taxonomy soon, so we'll reevaluate after that move.
Email is fine, or you can use our public chat at https://matrix.to/#/#OpenTreeOfLife_public:gitter.im

[Norlock]

Ok super thanks! I will join the matrix