Update fp-013-notification.md

[nataled]

[nataled]

I'm trying to modify a file but something keeps failing. For me to try again I have to make at least one change. This is a draft, even though I don't get the chance to mark it as one. Just ignore.

[cthoyt]

will need to update against master to pull in the flake8 issues that are causing the CI failures

[nataled]

Thanks for the heads-up. I'll wait until the work is finished (draft is still in progress).

[cthoyt]

Here's all ontologies with mailing lists:

prefix	name	mailing_list
bfo	Basic Formal Ontology	https://groups.google.com/forum/#!forum/bfo-discuss
obi	Ontology for Biomedical Investigations	http://groups.google.com/group/obi-users
aro	Antibiotic Resistance Ontology	https://mailman.mcmaster.ca/mailman/listinfo/card-l
cheminf	Chemical Information Ontology	https://groups.google.com/forum/#!forum/cheminf-ontology
chmo	Chemical Methods Ontology	[email protected]
cido	Coronavirus Infectious Disease Ontology	[email protected]
cl	Cell Ontology	https://groups.google.com/g/cl_edit
miapa	MIAPA Ontology	http://groups.google.com/group/miapa-discuss
mondo	Mondo Disease Ontology	https://groups.google.com/group/mondo-users
mop	Molecular Process Ontology	[email protected]
mp	Mammalian Phenotype Ontology	https://groups.google.com/forum/#!forum/phenotype-ontologies-editors
ms	Mass spectrometry ontology	[email protected]
ncro	Non-Coding RNA Ontology	[email protected], [email protected]
nomen	NOMEN - A nomenclatural ontology for biological names	https://groups.google.com/forum/#!forum/nomen-discuss
ohmi	Ontology of Host-Microbiome Interactions	http://groups.google.com/group/ohmi-discuss
ohpi	Ontology of Host Pathogen Interactions	http://groups.google.com/group/ohpi-discuss
ontoneo	Obstetric and Neonatal Ontology	http://groups.google.com/group/ontoneo-discuss
opmi	Ontology of Precision Medicine and Investigation	http://groups.google.com/group/opmi-discuss
ppo	Plant Phenology Ontology	[email protected]
ro	Relation Ontology	https://groups.google.com/forum/#!forum/obo-relations
rxno	Name Reaction Ontology	[email protected]
so	Sequence types and features ontology	https://sourceforge.net/p/song/mailman/song-devel/
uberon	Uberon multi-species anatomy ontology	https://lists.sourceforge.net/lists/listinfo/obo-anatomy
upheno	Unified phenotype ontology (uPheno)	https://groups.google.com/forum/#!forum/phenotype-ontologies-editors
xlmod	HUPO-PSI cross-linking and derivatization reagents controlled vocabulary	[email protected]
hp	Human Phenotype Ontology	https://groups.io/g/human-phenotype-ontology
gaz	Gazetteer	https://groups.google.com/forum/#!forum/obo-gazetteer

Code to generate this table:

from tabulate import tabulate
import requests
import yaml


def main():
    url = "https://raw.githubusercontent.com/OBOFoundry/OBOFoundry.github.io/master/registry/ontologies.yml"
    rows = []
    res = yaml.safe_load(requests.get(url).content)["ontologies"]
    for data in res:
        mailing_list = data.get("mailing_list")
        if mailing_list:
            rows.append((
                data["id"],
                data["title"],
                mailing_list,
            ))
    print(tabulate(rows, headers=["prefix", "name", "mailing_list"], tablefmt="github"))


if __name__ == '__main__':
    main()

[nataled]

@matentzn @cthoyt I'm at a loss as to what happened here. It looks like a huge number of commits were made to my branch by people other than me. I no longer need the version of the file indicated (it has been created/updated via another ticket), and certainly have no idea about all the other files that were changed. Do I just close this? Did all those 280+ file changes take effect in the master? I'd like to delete the branch but I have no idea what that will do to all this.

[cthoyt]

@nataled it looks like the commits from the main branch were merged improperly. Since this is a PR from one of your branches to the other, maybe you can try and update both of these two branches against the OBO Foundry's main branch and it might make it more obvious what were the unique changes

[matentzn]

No idea what happened here. I updated both of your branches, but they are totally scrambled. I have never seen anything like this! Can you restart the process?

[matentzn]

Actually it seems this branch has no changes on it. There must have been a syncining issue with merging between your branches. I think you can close this one here!

[nataled]

I'm not sure what process to restart. This branch began because I needed to edit a file and couldn't (at the time) figure out how to do it on the already-existing branch. That previous branch (16) has been dealt with already. This branch is definitely not needed by me, but 99.9% of the changes indicated are not mine.