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https://support.google.com/webmasters/answer/7489871?hl=en

I've noticed an unusual behavior in the PBDB with regard to mis-spelled taxon names. It seems that opinions that parent a mis-spelling to some higher taxon get returned in downloads (and are available in the search bar), but that opinions that correct a mis-spelling (but where the parent is the correctly spelled name instead of a higher taxon) are not available as obsolete names in downloads/search bar. The mis-spelled names seem to always be printed on taxon pages, however.

Here's an example:
Sepkoski had 3 versions of the trilobite genus Ascetopeltis (Ascetopeltis, Ascopeltis, and Acetopeltis). Here are the opinions:

If you download all names for Ascetopeltis : https://paleobiodb.org/data1.2/taxa/list.csv?datainfo&rowcount&base_name=Ascetopeltis&rank=genus&variant=all

you only get the names for Ascetopeltis (even if only search for invalid or obsolete names, and even if search for all opinions).

Similar, if you download the mis-spelled name/opinion: https://paleobiodb.org/data1.2/taxa/list.csv?datainfo&rowcount&base_name=Ascopeltis&rank=genus&variant=all

you return nothing.

In contrast, if a mis-spelled opinion was entered with a higher-taxon parent, such as Rhytidopilus:

Then the mis-spelled name gets returned in the download, and is also available as a redirect in the taxon search bar:
https://paleobiodb.org/data1.2/taxa/list.csv?datainfo&rowcount&base_name=Rhytidopilus&rank=genus&variant=all

Is this the expected behavior for downloads? It seems inconsistent to me.

Alternatively, is there some way to consistently download ALL obsolete mis-spelling of names (e.g., Ascopeltis) that point them to their accepted names?

Hi,

I've been looking up longhorn beetle fossils (Coleoptera: Cerambycidae) and found that when I search for 'Cerambycidae' the taxon page only lists one subfamily (Spondylinae), not the other seven! https://paleobiodb.org/classic/basicTaxonInfo?taxon_no=69413

Also, the taxon pages for Cerambycinae and Prioninae do not have any subtaxa listed (which the other subfamilies e.g. Lamiinae do) - the only way I could get to the cerambycine fossils was to search by genus, which is not ideal when you don't know what genera to look for.

The following API request:

https://paleobiodb.org/data1.2/occs/diversity.txt?base_name=Dinosauria&count=species

returns 187 sampled_in_bin results for the Cenomanian stage. Examining the 586 occurrences here:

https://paleobiodb.org/data1.2/occs/list.txt?base_name=dinosauria&interval=cenomanian

it appears that only 99 distinct species are actually present. The current result set includes all distinct accepted_name values, and does not limit the results to "accepted_rank = species". Consequently, the 187 sampled_in_bin results include distinct genera, families, etc.

This problem appears to be limited to the species count. Using the parameter "count=genera" in the diversity endpoint returns the correct count of 106 distinct genera (24 distinct values from accepted_rank = genera, plus 99 distinct values from accepted_rank species, minus the 17 repeated genera values from accepted_rank species).

It looks like the security certificate that allows https on paleobiodb.org expired yesterday. Because of this, I can't load it at all on Safari and Chrome gives me a warning and blocks the site unless I choose to circumvent it.

Entering 'bivalve', 'ammonite', 'vertebrate' returns an error in classic download generator.

The name 'vertebrate' did not match any name in the taxonomy table

Example:

https://paleobiodb.org/classic/basicCollectionSearch?collection_no=120887

This collection has two taxa, but only one displays. Both are visible on the edit screen, but the taxon that has been reidentified and assigned to an unranked clade does not appear except in edit mode.

Update the FAQ page to reflect recent changes to the database

• Update current funding and development team information.
• Update the bug reporting and feature requests to link to this issues page.
• Update the paleogeographic rotations information.

Search for "Costa" in the quick search. No genus returned, but there is a genus record:

https://paleobiodb.org/classic/checkTaxonInfo?taxon_no=24002

The Linnaean ranks are of limited utility, but there is an API route that aims to return canonical ranks for taxa. Many taxa are not classified in this scheme because sub- ranks are ignored. A good example is Decapoda < Malacostraca < Crustacea

In the PBDB representation, no crab is classified in any Linnaean sense, as Malacostraca is assigned "Subclass" status and Crustacea is assigned "Subphylum" status and its parent is a clade... with no Phylum rank in the mix.

I recommend elevating "sub" ranks when there is no exact rank for the Linnaean case. In every sense of the word except PBDB, Malacostraca is a Class. Seeing crabs as "unclassified" in the API response makes the data look bad (when in fact they are better).

When accessing the reidentifications form for an individual site, when I click "skip to next 10 occurrences" ... nothing happens. It looks like in the page coding the </a> is misplaced

<td align=center><b><a href="/classic/displayCollResults?type=reid&taxon_name=&collection_no=20327&sort_occs_by=created&sort_occs_order=asc&page_no=2"></a>Skip to the next 10 occurrences</b></td></tr>
<tr><td class=small align=center><i>Warning: if you go to the next page without saving, your changes will be lost</i></td>

Requested with March deadline by education grant participants.

• Choose and describe algorithms (@vjpsyverson)

• Implement in API (@mmcclenn)

• Make available via downloader (@vjpsyverson)

• (optional) Add to Navigator (@vjpsyverson)

In Navigator am I'm trying to generate a map with Bivalve, Echinoidea, and Gastropoda. However, whenever I search for and select Gastropoda, it clears my previously selected clades. For example:

1. Search and add Bivalve -- generates a map of just bivalve occurrences
2. Search and add Echinoidea -- adds to map fine
3. Search and add Gastropoda -- clears previous two taxa and only loads gastropoda

A related behavior happens if Gastropoda is added first. E.g.,

1. Search and add Gastropoda -- generates a map of just gastropod occurrences
2. Search and add Bivalve -- drops gastropods and generates a map of only bivalves
3. Search and add Actinopteri -- adds occurrences to bivalve map just fine

I haven't systematically searched, but it seems to be unique to the gastropods.

When using the PBDB Explorer and filtering on the Cenomanian stage, the system displays an occurrence count of 144395. When using the diversity end-point, a value of 20216 is returned for number of occurrences.

API Link:
https://paleobiodb.org/data1.2/occs/diversity.json?interval=mesozoic&base_name=life

Screenshots:

I am not a specialist, merely a Wikispecies user with an interest in nomenclatural matters (and particularly in clearing out homonym that are an actual practical issue on a wiki vs. a database). Between Wikispecies and IRMNG, there are quite a few homonyms I wish to report as either having been formally replaced (e.g. Acaroceras/Acaroceratidae) or in need of replacement (e.g. Aaleniella Conti & Fischer, 1981).

However, the FAQ is... unhelpful on these matters. All it says is "suggested corrections regarding individual data records should be sent directly to the contributor who authorized the data". And how exactly is a user even supposed to do that? Email everyone in turn hoping you eventually hit the right person?

As we discussed a few meetings ago, let's discuss a more logical naming system for the different PBDB repos.

We should have a streamlined FAQ discussing common data entry protocols.

Some examples of common questions:

1. What constitutes an occurrence in terms of spatiotemporal scale?
2. What constitutes a collection in terms of spatiotemporal scale?
3. If a trace fossil known to come from a specific organism is observed, should that organism be entered as an occurrence?
4. How should a biozone that is not recognized by the PBDB be entered?
5. How should enterers handle taxonomic names that are known to be incorrect or misspelled?

etc....

I believe this is an area where we could solicit members of the community (authorizers) to submit questions they frequently encounter when training students/enterers.

On the Reference Seach Form
https://paleobiodb.org/classic/displaySearchRefs?type=view
I searched for Author's name equals 'Pomel'
That returned 8 references.
On 'A. Pomel, 1886' I clicke on '3 taxonomic names'
Got the following: "Can not open template add_enter_authority"
I tried some of the other returned references, this only seems to happen for those with no opinion or collection listed.

Hi!

I've been trying to download the references from the database for a while now but I seem to be unable to get a complete list:

It's always timing out if I go for this:
https://paleobiodb.org/data1.2/taxa/refs.txt?datainfo&rowcount&base_name=Life&select=occs
but works if I filter by time intervals, e.g.
https://paleobiodb.org/data1.2/occs/refs.csv?interval=Ediacaran,Holocene&select=ops&show=formatted,entname

But I only seem to be able to download references for occurrences but not for the other categories (collections, opinions,...)

Ticking the option "Select all bibliographic reference records in the database" also doesn't work

Attention all @paleobiodb/owners, here are the following suggested renames of repos. Changing the repo names will make things easier to follow and understand. This WILL NOT break branches under the repos or files and directory names on local disks so no worries.

Old -> New
navigator -> Navigator
pbdb-main -> SplashPage
pbdb-new -> DataService
beta-testing-group -> BetaTesters
pbdb-wing -> WebApp
paleobiodb_utilities -> AnalysisTools
teachPaleobiology -> Suggest move to @aazaff personal repo
Wing -> This is a fork, leave as is
larkin -> Larkin or leave as is
pbdb_changelog -> ChangeLog
pbdb-classic -> Original-PBDB-Codebase
pdd -> Do we need this fork here, there have been no commits from our group to it. If yes please write a readme for it because we don't know what it is.

Comment on this issue by the end of the week, @jpjenk will make these changes Friday afternoon.

Navigator appears to not open! It just gets stuck "Initializing"

We do need a solution for binning the occurrence data to a current time scale that can be downloaded alongside the occurrence data. At the minimum I'd propose to at least re-assinging the old 11 myr bins to each collection (and publish this binning scheme too).
Thanks and best
Wolfgang

Hi! I was playing with the references table from paleodb, and noticed errors in some of records:

• references 12845, 23896, 64178 have publication year set in future
• there are DOIs associated with more that one reference:
  10.1016/j.cretres.2008.02.002
  10.1130/0016-7606
  10.1144/GSL.JGS.1853.009.01-02.19
  10.1080/03115510701305173
  10.1671/0272-4634
  10.1371/journal.pone.0038900
  10.1017/S1755691010009266
  10.3402/polar.v30i0.7265
  10.1016/j.annpal.2012.04.001
  10.1163/1876312X-45032121
  10.1016/j.crpv.2014.03.008
  10.1098/rspb.2009.1178
  10.1111/j.1475-4983.2012.01159.x
  10.1016/j.palaeo.2013.05.012
  10.1080/02724634.2010.522432
  10.1007/s10914-015-9292-y
  10.1144/sjg2015-005
  10.1080/03115510108619233
  10.1038/srep40691
  10.11646/zootaxa.3826.1.3
  10.1371
  10.1111/ede.12076
  10.1016/j.jsames.2018.11.015
  10.1080/08912963.2016.1248434
  10.7717/peerj.1171
  10.4072/rbp.2014.3.12
  10.1080/14772019.2017.1394922
  10.1306/M19375C20
  10.1007/s00606-013-0886-7
  10.1016/j.ympev.2010.08.024
  10.1007/s12542-013-0193-1
  10.5710/AMGH.23.07.2015.2856
  10.1371/journal.pone.0128871

There's a mismatch between the paleocoordinates when you search for a collection in the database versus when they're downloaded, i.e. the two are using different rotations. For example, PBDB collection # 34645 gives paleocoordinates of 31.1° N, 59.6° E if you search on PBDB (or Fossilworks), but if you download the collection you get 53.31º N, 83.24º E:

API: https://paleobiodb.org/data1.2/colls/list.csv?datainfo&rowcount&coll_id=34645&private&show=paleoloc

Search: https://paleobiodb.org/classic?a=basicCollectionSearch&collection_no=34645

This is an extreme example as the collection is on a plate boundary, but presumably it affects all collections at least a small amount.

On a correctly displaying page, references for additional taxon occurrences (secondary references) display at the bottom (e.g., https://paleobiodb.org/classic/basicCollectionSearch?collection_no=18140). Other lists do not (https://paleobiodb.org/classic/basicCollectionSearch?collection_no=190942), and I can't see any way for some one who isn't logged into the system as a user to even be able to determine which occurrences are from non-primary references.

Data download is broken on the site.

When you search on the app for Proboscideans, it changes the class to Insects. Also trying to pull records out the database using Proboscidea returns insect records.

It is not entirely clear why we are returning no data for this call:
https://paleobiodb.org/data1.2/colls/summary.json?show=time&min_ma=278&max_ma=282&level=3

When trying to download species data from the family Stegodontidae, only one species is returned, despite 30 being visible on the Stegodontidae page - I think the species names haven't been fully entered. Setting the resolution to 'all' instead of 'species' returns everything, with some occurrences having "tdf": "species not entered", despite a species name listed under "idn".

When toggling the Taxa Browser in the PBDB Navigator, number of listed sub-taxa seems to be capped at 10. For example, if searching for Phylum Arthropoda, toggling the taxa browser "on" shows the following:

Additionally, it does not seem to parse out the taxa based on what time period is selected in the Navigator. So having the filters "Arthropoda" and "Permian" active does not seem to change the results in the taxa browser.

this is only a test

I created a 'master' collection to include a number of collections within an umbrella. If I search for that master collection, and I go to the full details and then to metadata and references, I can see that there are other collections that are a subset. However, when I try to download this 'master' collection, it does NOT download the occurrence data from those subset collections. It also isn't clear in the 'basic' collections search that there are subset collections.

Downloading data for the Triassic Period I observed that taxa from from Longobardian were assigned a minimum age of 235 while the Ladinian is assigned a minimum age of 237. I believe the Longobardian is the younger interval of the Ladinian, and so it should end at 237.

The author and date for Dipoides williamsi is correctly given as Stirton 1936, but the linked reference is for a different publication from the same year. The correct paper in which this species is named is Stirton RA 1936 A new beaver from the Pliocene of Arizona with notes on the species of Dipoides. Journal of Mammalogy 17(3):279-281

Genus of bivalves, Donax (Linnaeus, 1758), are misclassified under Monocotyledoneae - Zingiberales - Zingiberidae. Due to this error, when you search for the family "Donacidae" on paleobiodb none of the Donax specimens are included in the results. When you search "Donax" and click on a collection/specimen, all the linked references in the database appear correct (state they are are bivalves/molluscs etc), but the donax species is listed under Monocotyledoneae. E.g.
https://paleobiodb.org/classic/displayCollResults?taxon_no=142233&max_interval=Quaternary&country=Ireland&is_real_user=1&basic=yes&type=view&match_subgenera=1

I thought maybe there was an update. It's been 24 hours now and still nothing works.

504 server for all species, all sites. Searches are just "Error something went wrong."

1. Do we want people to file bugs in the service-appropriate repository (e.g., navigator bugs in the navigator repository), or all bugs in this repository?

2. Also, what about enhancement requests or questions as opposed to bug reporting?

https://paleobiodb.org is currently showing an invalid SSL certificate & when I try to navigate to "Download Data" I get the following error:

502 Bad gateway. Invalid response from upstream server

As of 9:00 AM 12/2/2016

• the login page does not load
• the contact us page is not updated to reflect the new sign up system.
• the change log is not displaying on the splash page.

The download form and login are down, 502 error.

When executing the following request:

https://paleobiodb.org/data1.2/occs/list.json?base_name=dinosauria&interval=cenomanian

The following record does not return, despite apparently qualifying based on the parameters:

https://paleobiodb.org/classic/checkTaxonInfo?taxon_no=68418&is_real_user=1

Modifying the request to check other stages in the possible range (Turonian and Santonian) doesn't return the record either.

When I enter a taxon name into the text box in the upper right corner of the Classic interface, it is returning collections containing that taxon, rather than the typical "taxon page." The only way I have found to access the taxon page is to click on a collection, then click on the name of the taxon in the occurrences.

Not sure if this is because the resources were never made, but all the subheadings here: https://paleobiodb.org/#/resources (Web Apps, Mobile Apps, Lesson Plans, etc) don't link to anything. This is the case on both Chrome and Firefox in Ubuntu.

Thanks!

testing slack integration

When you view a collection, it does not show the minimum age correctly. For example, PBDB collection #56683 shows the age as Kimmeridgian to Kimmeridgian, when the collection is Kimmeridgian to Tithonian (which can be seen when editing the collection). The minimum age is correctly shown in terms of Ma though.

Simia Mikhailova and Jankauskas 1989 (acritarch) is not equal to Simia Linnaeus 1758 (primate; now suppressed). Due to this error, primates and all parent taxa are listed as having Ediacaran origin.

Collections with Simia Mikhailova and Jankauskas 1989:

• https://paleobiodb.org/classic/basicCollectionSearch?collection_no=221270
• https://paleobiodb.org/classic/basicCollectionSearch?collection_no=221354

When creating a new reference there is a tip sheet link related to the taxonomy field. The information presented seems to be related to classification of publications.

https://paleobiodb.org/classic?action=displayPage&page=classification_quality

My expectation would be to see guidance related to the four elements presented in the Taxonomy drop-down so that I can select the correct value. As a relative neophyte (the type of person who might most need a tip sheet), the information presented doesn't help me understand the four possible values.

The main API documentation page loads when the following are entered into the web address bar: https://paleobiodb.org/data1.2/index.html, https://paleobiodb.org/data1.2/index, https://paleobiodb.org/data1.2/

However, when the trailing slash is omitted (https://paleobiodb.org/data1.2), a 404 error is returned.

This seems like new behavior and is non-intuitive for many users. Perhaps a redirect was dropped?

I reproduced this error on Mac OS Catalina using the latest versions of Safari and Firefox.