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mite taxon [Penthaleus major] mentioned twice in TPT Acari taxonomy #22

Open jhpoelen opened 1 year ago

jhpoelen commented 1 year ago

when using recently introduced tpt taxonomy support in Nomer, I found that looking up taxonomic name alignments for Penthaleus major via:

echo -e "\tPenthaleus major" | nomer append tpt --include-header

yielded in two results:

providedExternalId providedName relationName resolvedExternalId resolvedName resolvedAuthorship resolvedRank resolvedCommonNames resolvedPath resolvedPathIds resolvedPathNames resolvedPathAuthorships resolvedExternalUrl
Penthaleus major HAS_ACCEPTED_NAME acari_2131880 Penthaleus major (A. L. Dugès, 1834) species Animalia | Arthropoda | Arachnida | Trombidiformes | Penthaleidae | Penthaleus | major kingdom | phylum | class | order | family | genus | specificEpithet
Penthaleus major HAS_ACCEPTED_NAME acari_7686008 Penthaleus major A. L. Dugès, 1834 species Animalia | Arthropoda | Arachnida | Trombidiformes | Penthaleidae | Penthaleus | major kingdom | phylum | class | order | family | genus | specificEpithet

@EMTuckerLab @njdowdy is it expected that Penthaleus major has two hits in the TPT Acari taxonomy?

njdowdy commented 1 year ago

The entry with acari_7686008 would seem to be an error to me. The original name appears to have been Tetranychus major A. L. Dugès, 1834 which was subsequently moved to Penthaleus major (A. L. Dugès, 1834). So Penthaleus major A. L. Dugès, 1834 does not appear to me to be a valid entity.

But perhaps there is a complicated situation here and an acari expert should be consulted to verify?

njdowdy commented 1 year ago

Checking further, there may be some bigger problems with this taxon. From GBIF remarks (https://www.gbif.org/species/148901462):

"Publ.: ""as T. majeur"", Dugès, A., 1834: 57, seen. The name major is not mentioned in the article. Is it a valid name at all?"

I think calling in an expert to verify this one with the original publication is a great idea.

EMTuckerLab commented 1 year ago

It does appear that the acari_7686008 https://www.gbif.org/species/7686008 entry got messed up and should have been Tetranychus major A. L. Dugès and listed as a synonym (that's what is listed for gbif's id number https://www.gbif.org/species/7686008). Penthaleus major (A. L. Dugès, 1834) certainly appears valid though and is apparently a well known mite with wikipedia pages and everything (aka the winter grain mite). We can email Barry to double check, but I think fixing the acari_7686008 entry to reflect T. major as a synonym would work?

Erika Tucker, PhD (she/her/hers) Milwaukee Public Museum | TPT https://parasitetracker.org/Taxonomy https://parasitetracker.org/Digitization Manager https://parasitetracker.org/ Biodiversity Outreach Network (BON) https://www.bon-earth.org/ | Research Associate https://www.bon-earth.org/about-us | S2 Administrative Manager https://www.bon-earth.org/_files/ugd/68d22d_372c2df8960041a1a5328b5e43c7b3c3.pdf Entomologist, Museum Specialist, & Researcher ORCiD 0000-0002-8822-2315 https://orcid.org/0000-0002-8822-2315

Check it out! Bug.News http://bug.news/ (blog) TPT Resource Hub https://bit.ly/TPTresourceHub (taxonomy) GloBI How-To https://www.globalbioticinteractions.org/how-to (help page) Entomological Resources https://www.bon-earth.org/products-resources (supplies, DIY, etc.) BugFlow https://entcollnet.github.io/BugFlow/ (digitization workflows) Brood X & Spotted Lanternfly Jewelry https://www.earthengypsydesigns.com/category/bugs!

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On Mon, Dec 19, 2022 at 10:12 AM Dr. Nicolas J. Dowdy < @.***> wrote:

Checking further, there may be some bigger problems with this taxon. From GBIF remarks (https://www.gbif.org/species/148901462):

"Publ.: ""as T. majeur"", Dugès, A., 1834: 57, seen. The name major is not mentioned in the article. Is it a valid name at all?"

I think we calling in an expert to verify this one with the original publication is a great idea.

— Reply to this email directly, view it on GitHub https://github.com/njdowdy/tpt-taxonomy/issues/22#issuecomment-1357816918, or unsubscribe https://github.com/notifications/unsubscribe-auth/AN2RXUOGO44EMT6DC36C7CLWOB3O5ANCNFSM6AAAAAATDOQFCU . You are receiving this because you were mentioned.Message ID: @.***>

jhpoelen commented 1 year ago

@njdowdy @EMTuckerLab thanks for your prompt replies .

Just to be precise and accurate on my earlier observations -

the tpt taxonomy version was the most recent one included in

Poelen, Jorrit H. (2022). Nomer Corpus of Taxonomic Resources hash://sha256/dac5911a81fb605fab012e90c98b37e990a076d77f9264fdb38ec7f379d82108 hash://md5/46fab6751bafd4de4f49aaa8c511e39d (0.9) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7405576

as indexed by Nomer v0.4.7

with alias:

$ preston alias https://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/Acari/Acari-standardized-v2.csv
<https://raw.githubusercontent.com/njdowdy/tpt-taxonomy/main/Acari/Acari-standardized-v2.csv> <http://purl.org/pav/hasVersion> <hash://sha256/f94949369cb6625b05d3d7013d6ed0ea6302be166016b025cbcd19b4ee92b5da> <urn:uuid:f7eb0d94-4173-4191-918a-f4a91cc39b96> .

See also attached content generated via

preston cat hash://sha256/f94949369cb6625b05d3d7013d6ed0ea6302be166016b025cbcd19b4ee92b5da > f94949369cb6625b05d3d7013d6ed0ea6302be166016b025cbcd19b4ee92b5da.csv

f94949369cb6625b05d3d7013d6ed0ea6302be166016b025cbcd19b4ee92b5da.csv

and associated lines 40195 and 40196 referenced in this issue:

$ preston cat hash://sha256/f94949369cb6625b05d3d7013d6ed0ea6302be166016b025cbcd19b4ee92b5da | grep -nP "acari_7686008|acari_2131880"
40195:GBIF,acari_2131880,,,2131879,7686008,,,,"Penthaleus major (A. L. Dugès, 1834)",,,,,Checklist of Norwegian ticks and mites (Acari). Fauna norv. Ser. B 26:31-45,,,Animalia,Arthropoda,Arachnida,,,Trombidiformes,,,,,,Penthaleidae,,,,Penthaleus,,major,,species,,"(A. L. Dugès, 1834)",,,accepted,,,Penthaleus major
40196:GBIF,acari_7686008,,2131880,2131879,,,,,"Tetranychus major A. L. Dugès, 1834",Penthaleus major,,,,,,,Animalia,Arthropoda,Arachnida,,,Trombidiformes,,,,,,Penthaleidae,,,,Penthaleus,,major,,species,,"A. L. Dugès, 1834",,,homotypic synonym,,,Tetranychus major

more specifically, 

preston cat 'line:hash://sha256/f94949369cb6625b05d3d7013d6ed0ea6302be166016b025cbcd19b4ee92b5da!/L40196'

yielding 

GBIF,acari_7686008,,2131880,2131879,,,,,"Tetranychus major A. L. Dugès, 1834",Penthaleus major,,,,,,,Animalia,Arthropoda,Arachnida,,,Trombidiformes,,,,,,Penthaleidae,,,,Penthaleus,,major,,species,,"A. L. Dugès, 1834",,,homotypic synonym,,,Tetranychus major

and 

preston cat 'line:hash://sha256/f94949369cb6625b05d3d7013d6ed0ea6302be166016b025cbcd19b4ee92b5da!/L40195'

yielding

GBIF,acari_2131880,,,2131879,7686008,,,,"Penthaleus major (A. L. Dugès, 1834)",,,,,Checklist of Norwegian ticks and mites (Acari). Fauna norv. Ser. B 26:31-45,,,Animalia,Arthropoda,Arachnida,,,Trombidiformes,,,,,,Penthaleidae,,,,Penthaleus,,major,,species,,"(A. L. Dugès, 1834)",,,accepted,,,Penthaleus major
jhpoelen commented 1 year ago

@njdowdy @EMTuckerLab this makes me wonder . . . how to document this future correction to the TPT Acari taxonomy so that folks can see exact what and why was changed between the different versions of the TPT Acari (without having to revert to highly technical git commit logs)?

Similar how-to-annotate example see https://github.com/jhpoelen/msw-plazi/issues/1 .

EMTuckerLab commented 1 year ago

Hmm - could a "Changes" or "Updates" column be auto generated? Then we could just have categories or short sentences in the column like, "Line/name merging error fix. See link to github comments for more info", or "Name miscategorization fix. See link to github comments for more info.". Something like that? Or is that creating more work instead of less?

Erika Tucker, PhD (she/her/hers) Milwaukee Public Museum | TPT https://parasitetracker.org/Taxonomy https://parasitetracker.org/Digitization Manager https://parasitetracker.org/ Biodiversity Outreach Network (BON) https://www.bon-earth.org/ | Research Associate https://www.bon-earth.org/about-us | S2 Administrative Manager https://www.bon-earth.org/_files/ugd/68d22d_372c2df8960041a1a5328b5e43c7b3c3.pdf Entomologist, Museum Specialist, & Researcher ORCiD 0000-0002-8822-2315 https://orcid.org/0000-0002-8822-2315

Check it out! Bug.News http://bug.news/ (blog) TPT Resource Hub https://bit.ly/TPTresourceHub (taxonomy) GloBI How-To https://www.globalbioticinteractions.org/how-to (help page) Entomological Resources https://www.bon-earth.org/products-resources (supplies, DIY, etc.) BugFlow https://entcollnet.github.io/BugFlow/ (digitization workflows) Brood X & Spotted Lanternfly Jewelry https://www.earthengypsydesigns.com/category/bugs!

https://www.earthengypsydesigns.com/product/17yr-cicada-wings-fw-necklace-stones https://www.earthengypsydesigns.com/product/17yr-cicada-wings-h2 https://www.earthengypsydesigns.com/product/spotted-lanternfly-framed-teardrop-hw https://www.earthengypsydesigns.com/product/spotted-lanternfly-earrings-fw-pearl

On Mon, Dec 19, 2022 at 10:28 AM Jorrit Poelen @.***> wrote:

@njdowdy https://github.com/njdowdy @EMTuckerLab https://github.com/EMTuckerLab this makes me wonder . . . how to document this future correction to the TPT Acari taxonomy so that folks can see exact what and why was changed between the different versions of the TPT Acari (without having to revert to highly technical git commit logs).

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jhpoelen commented 1 year ago

btw - please note that the offending line:

GBIF,acari_7686008,,2131880,2131879,,,,,"Tetranychus major A. L. Dugès, 1834",Penthaleus major,,,,,,,Animalia,Arthropoda,Arachnida,,,Trombidiformes,,,,,,Penthaleidae,,,,Penthaleus,,major,,species,,"A. L. Dugès, 1834",,,homotypic synonym,,,Tetranychus major

does mention Tetranychus major along with the note relating to a homotypic synonym. Perhaps this is just a Nomer bug in interpretation of tpt taxonomic tables?

Can you please confirm that the tpt acari taxonomy line 40196 is as expected? And if so, can you please help me understand why the taxonomic hierarchy for Penthaleus major was included in line 40196, but not its original?

jhpoelen commented 1 year ago

re: annotations

Hmm - could a "Changes" or "Updates" column be auto generated? Then we could just have categories or short sentences in the column like, "Line/name merging error fix. See link to github comments for more info", or "Name miscategorization fix. See link to github comments for more info.". Something like that? Or is that creating more work instead of less?

Github comments are typically not published, and/or easily accessible outside of specialized tools requiring special technical knowledge. So, yes, the changes are tracked, but, they are not easily accessible. Similar to changes in wikipedia / wikidata are tracked, but they are published in a different way than the actual content and hidden away in some kind of "history" table.

Perhaps one way to go about it is to keep an annotation table similar to the prototype at https://github.com/jhpoelen/msw-plazi/blob/main/annotations.csv .

This table includes a human readable account of what changed into what, who made/proposed the edit, and when, along with a secure, machine readable reference to the exact versions and location of the text that was updated.

This annotations.csv would be kept along with the full tables as a record of editorial decisions made.

Curious to hear your thoughts.

EMTuckerLab commented 1 year ago

Oh! Looking at the whole line in the file, that actually looks correct I think. It has Tetranychus major A. L. Dugès, 1834 listed as a scientific name that exists, which it is whether or not its valid, and it lists Penthaleus major as the accepted name (as well as ID number in the id number fields). I would have had the genus column match the genus in the scientific name column instead of the accepted name, but I don't know that that's a big deal.

Erika Tucker, PhD (she/her/hers) Milwaukee Public Museum | TPT https://parasitetracker.org/Taxonomy https://parasitetracker.org/Digitization Manager https://parasitetracker.org/ Biodiversity Outreach Network (BON) https://www.bon-earth.org/ | Research Associate https://www.bon-earth.org/about-us | S2 Administrative Manager https://www.bon-earth.org/_files/ugd/68d22d_372c2df8960041a1a5328b5e43c7b3c3.pdf Entomologist, Museum Specialist, & Researcher ORCiD 0000-0002-8822-2315 https://orcid.org/0000-0002-8822-2315

Check it out! Bug.News http://bug.news/ (blog) TPT Resource Hub https://bit.ly/TPTresourceHub (taxonomy) GloBI How-To https://www.globalbioticinteractions.org/how-to (help page) Entomological Resources https://www.bon-earth.org/products-resources (supplies, DIY, etc.) BugFlow https://entcollnet.github.io/BugFlow/ (digitization workflows) Brood X & Spotted Lanternfly Jewelry https://www.earthengypsydesigns.com/category/bugs!

https://www.earthengypsydesigns.com/product/17yr-cicada-wings-fw-necklace-stones https://www.earthengypsydesigns.com/product/17yr-cicada-wings-h2 https://www.earthengypsydesigns.com/product/spotted-lanternfly-framed-teardrop-hw https://www.earthengypsydesigns.com/product/spotted-lanternfly-earrings-fw-pearl

On Mon, Dec 19, 2022 at 11:11 AM Jorrit Poelen @.***> wrote:

re: annotations

Hmm - could a "Changes" or "Updates" column be auto generated? Then we could just have categories or short sentences in the column like, "Line/name merging error fix. See link to github comments for more info", or "Name miscategorization fix. See link to github comments for more info.". Something like that? Or is that creating more work instead of less?

Github comments are typically not published, and/or easily accessible outside of specialized tools requiring special technical knowledge. So, yes, the changes are tracked, but, they are not easily accessible. Similar to changes in wikipedia / wikidata are tracked, but they are published in a different way than the actual content and hidden away in some kind of "history" table.

Perhaps one way to go about it is to keep an annotation table similar to the prototype at https://github.com/jhpoelen/msw-plazi/blob/main/annotations.csv .

This table includes a human readable account of what changed into what, who made/proposed the edit, and when, along with a secure, machine readable reference to the exact versions and location of the text that was updated.

This annotations.csv would be kept along with the full tables as a record of editorial decisions made.

Curious to hear your thoughts.

— Reply to this email directly, view it on GitHub https://github.com/njdowdy/tpt-taxonomy/issues/22#issuecomment-1357900010, or unsubscribe https://github.com/notifications/unsubscribe-auth/AN2RXUPPD6FSK5PQ362YCZ3WOCCJXANCNFSM6AAAAAATDOQFCU . You are receiving this because you were mentioned.Message ID: @.***>

jhpoelen commented 1 year ago

@EMTuckerLab Thanks for double checking. Before I file some bug on Nomer, I'd like to better understand how to interpret the tpt acari table.

Are you saying that the parsed out hierarchy of Tetranychus major includes the accepted name, and not the original synonym. But how would you be able to match an outdated hierarchy? I am assuming that you'd want the full hierarchy for the synonym also correct?

jhpoelen commented 1 year ago

From the last three lines in TPT Acari, it appears that only the accepted name hierarchy is parsed out, and only the scientific / canonical name of the synonym is mentioned. 

<line:hash://sha256/f94949369cb6625b05d3d7013d6ed0ea6302be166016b025cbcd19b4ee92b5da!/L48135> <http://www.w3.org/ns/prov#value> "GBIF,acari_8090574,,2180376,2180362,,,,,\"Acarus ypsilophora Bonz, 1783\",Unionicola ypsilophora,,,,,,,Animalia,Arthropoda,Arachnida,,,Trombidiformes,,,,,,Unionicolidae,,,,Unionicola,,ypsilophora,,species,,\"Bonz, 1783\",,,homotypic synonym,,,Acarus ypsilophora" <urn:uuid:34873b00-1e57-487b-ac01-325d933e654a> .
<line:hash://sha256/f94949369cb6625b05d3d7013d6ed0ea6302be166016b025cbcd19b4ee92b5da!/L48136> <http://www.w3.org/ns/prov#value> "GBIF,acari_7418058,,2180376,2180362,8090574,,,,\"Atax ypsilophorus (Bonz, 1783)\",Unionicola ypsilophora,,,,,,,Animalia,Arthropoda,Arachnida,,,Trombidiformes,,,,,,Unionicolidae,,,,Unionicola,,ypsilophorus,,species,,\"(Bonz, 1783)\",,,synonym,,,Atax ypsilophorus" <urn:uuid:34873b00-1e57-487b-ac01-325d933e654a> .
<line:hash://sha256/f94949369cb6625b05d3d7013d6ed0ea6302be166016b025cbcd19b4ee92b5da!/L48176> <http://www.w3.org/ns/prov#value> "GBIF,acari_6924479,,4541598,2180950,,,,,\"Tiphys podagricus Koch, 1837\",Wettina podagrica,,,,,,,Animalia,Arthropoda,Arachnida,,,Trombidiformes,,,,,,Wettinidae,,,,Wettina,,podagricus,,species,,\"Koch, 1837\",,,homotypic synonym,,,Tiphys podagricus" <urn:uuid:34873b00-1e57-487b-ac01-325d933e654a> .

can you confirm?

jhpoelen commented 1 year ago

e.g.,

Acarus ypsilophora Bonz, 1783 SYNONYM_OF Unionicola ypsilophora Bonz, 1783

?

jhpoelen commented 1 year ago

But . . . shouldn't the authorship of the accepted name hierarchy be in parenthesis?

e.g.,

Unionicola ypsilophora (Bonz, 1783)

jhpoelen commented 1 year ago

I am probably misunderstanding your format - thanks for taking the time to help me better understand the rationale behind the format.

EMTuckerLab commented 1 year ago

I have another meeting at the moment, but I could jump on zoom/google chat later this afternoon (after 3pm est) if screen sharing would help? Otherwise, I'll just keep responding via email once my meeting ends :)

Erika Tucker, PhD (she/her/hers) Milwaukee Public Museum | TPT https://parasitetracker.org/Taxonomy https://parasitetracker.org/Digitization Manager https://parasitetracker.org/ Biodiversity Outreach Network (BON) https://www.bon-earth.org/ | Research Associate https://www.bon-earth.org/about-us | S2 Administrative Manager https://www.bon-earth.org/_files/ugd/68d22d_372c2df8960041a1a5328b5e43c7b3c3.pdf Entomologist, Museum Specialist, & Researcher ORCiD 0000-0002-8822-2315 https://orcid.org/0000-0002-8822-2315

Check it out! Bug.News http://bug.news/ (blog) TPT Resource Hub https://bit.ly/TPTresourceHub (taxonomy) GloBI How-To https://www.globalbioticinteractions.org/how-to (help page) Entomological Resources https://www.bon-earth.org/products-resources (supplies, DIY, etc.) BugFlow https://entcollnet.github.io/BugFlow/ (digitization workflows) Brood X & Spotted Lanternfly Jewelry https://www.earthengypsydesigns.com/category/bugs!

https://www.earthengypsydesigns.com/product/17yr-cicada-wings-fw-necklace-stones https://www.earthengypsydesigns.com/product/17yr-cicada-wings-h2 https://www.earthengypsydesigns.com/product/spotted-lanternfly-framed-teardrop-hw https://www.earthengypsydesigns.com/product/spotted-lanternfly-earrings-fw-pearl

On Mon, Dec 19, 2022 at 11:27 AM Jorrit Poelen @.***> wrote:

I am probably misunderstanding your format - thanks for taking the time to help me better understand the rationale behind the format.

— Reply to this email directly, view it on GitHub https://github.com/njdowdy/tpt-taxonomy/issues/22#issuecomment-1357922454, or unsubscribe https://github.com/notifications/unsubscribe-auth/AN2RXUMTVBLN2OWHOSHKEBDWOCEGDANCNFSM6AAAAAATDOQFCU . You are receiving this because you were mentioned.Message ID: @.***>

jhpoelen commented 1 year ago

A zoom chat would be nice. I'll checkin at 3pm est.

jhpoelen commented 1 year ago

Another note:

It appears that Tetranychus major has not only relations to Penthaleus major , but also to Tetranychus urticae .

<urn:uuid:e52d9ec2-a074-42be-8875-c552d272b3f6> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> <urn:uuid:e52d9ec2-a074-42be-8875-c552d272b3f6> .
<urn:uuid:e52d9ec2-a074-42be-8875-c552d272b3f6> <http://www.w3.org/ns/prov#used> <hash://sha256/f94949369cb6625b05d3d7013d6ed0ea6302be166016b025cbcd19b4ee92b5da> <urn:uuid:e52d9ec2-a074-42be-8875-c552d272b3f6> .
<urn:uuid:e52d9ec2-a074-42be-8875-c552d272b3f6> <http://purl.org/dc/terms/description> "An activity that finds the locations of text matching the regular expression 'Tetranychus major' inside any encountered content (e.g., hash://sha256/... identifiers)."@en <urn:uuid:e52d9ec2-a074-42be-8875-c552d272b3f6> .
<line:hash://sha256/f94949369cb6625b05d3d7013d6ed0ea6302be166016b025cbcd19b4ee92b5da!/L40196> <http://www.w3.org/ns/prov#value> "GBIF,acari_7686008,,2131880,2131879,,,,,\"Tetranychus major A. L. Dugès, 1834\",Penthaleus major,,,,,,,Animalia,Arthropoda,Arachnida,,,Trombidiformes,,,,,,Penthaleidae,,,,Penthaleus,,major,,species,,\"A. L. Dugès, 1834\",,,homotypic synonym,,,Tetranychus major" <urn:uuid:e52d9ec2-a074-42be-8875-c552d272b3f6> .
<line:hash://sha256/f94949369cb6625b05d3d7013d6ed0ea6302be166016b025cbcd19b4ee92b5da!/L45566> <http://www.w3.org/ns/prov#value> "GBIF,acari_2130196,,2130185,2130777,,,,,\"Tetranychus major Donnadieu, 1875\",Tetranychus urticae,,,,\"Donnadieu, A. L. Recherches pour servir a l'histoire des Tetranyques. Annales de la Societe Linneenne de Lyon (n. ser. ), 22: 29-136. (1875). \",,,Animalia,Arthropoda,Arachnida,,,Trombidiformes,,,,,,Tetranychidae,,,,Tetranychus,,major,,species,,\"Donnadieu, 1875\",,,heterotypic synonym,,,Tetranychus major" <urn:uuid:e52d9ec2-a074-42be-8875-c552d272b3f6> .
jhpoelen commented 1 year ago

In discussion with @EMTuckerLab , we thought it may be nice to upgrade the column hierarchical level and authorship to be prefixed with "accepted" or "original" (or something similar). This way naive parsers can distinguish between taxonomic information associated with their accepted name vs. the alternative name.

jhpoelen commented 1 year ago

from https://dwc.tdwg.org/list/#dwc_Taxon (see below), note that no term for e.g., acceptedGenus exists

image

jhpoelen commented 1 year ago

Note that for Phthiraptera taxonomy, the name columns (genus, etc) do not point to the accepted name of a assumed synonym like the one documented in https://github.com/globalbioticinteractions/nomer/issues/138 . This makes the Phthiraptera darwin core compliant.

jhpoelen commented 1 year ago

Also, for Siphonaptera taxonomy the taxonomic fields are darwincore compliant and do not seem to document the taxonomic information of the accepted name. The accepted name is document in the fields prefixed with "accepted..."

jhpoelen commented 1 year ago

Neither Aves nor Mammalia TPT taxonomies appears to document synonyms. Aves did have taxonomicStatus, and all values were "accepted."