Manage data about taxonomy
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This page contains general information about community practices for managing data about taxonomy, and also aggregates links to additional resources with more specific information.
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Taxonomic data are stored differently in different Collections Management Systems. Options include:
- Multiple flat hierarchical trees for each taxon (Arctos, Symbiota)
- Hierarchy through parent-child relationships, with stepchildren / synonymsDifferent scientific name referring to the same taxon. (MS SQLServer, Specify)
- Hierarchy through parent-child relationships (EMu, Specify)
- Fields for each rank that are not connected - flat structure (MCZbase, Access)
- Pseudo-hierarchy - not explicitly linked across entries in tree (EMu - NMNH)
Taxonomic authorities are a critical resource for collections management because they provide information about valid and invalid names curated by taxonomic experts. Different general strategies for using taxonomic authorities include:
- For a given species identification in the collection, use the taxonomic authorityThe author(s) who formally published the scientific name of a taxon, often included after the species name. to get information about higher taxonomy, e.g. family level and above.
- Look up synonymous names in the taxonomic authority.
- Create a custom taxonomic dictionary on other existing taxonomy authorities.
- Track opinions from taxonomic authority as a way to provide more information about the validity (or lack thereof) of specimen identifications.
- Include links to identifiers maintained by a taxonomic authority (e.g. AphiaIDs from WoRMSWorld Register of Marine Species. Authoritative taxonomy database for global marine species.) for taxon conceptsThe circumscription of what a taxon name refers to in a particular context since interpretations may differ.
Including scientific authorship alongside the taxonomy for species-level identifications is a common practice in paleo collections, and an important way to disambiguate homonyms across the broader landscape of neontological and fossil taxonomy.
Across paleo collections, we lack a good method for dealing with higher classification for taxa where this is unknown, e.g. for many ichnofossils. The most common strategy is to leave fields related to higher classification blank, although some collections prefer to record “incertae sedis, “or “indet.”/”indeterminate” in these fields. The ICZNInternational Code of Zoological Nomenclature. Governing set of rules for the naming of animals and the resolution of nomenclatural problems. (1999) recognizes “incertae sedis” but recommends attaching the highest known taxonomic level, e.g. “Cephalopoda incertae sedis.”
Unranked cladesA group of organisms consisting of a common ancestor and all its descendants. also pose a challenges in fossil taxonomy. Not only are many databases unable to handle the data structure of unranked clades, but it can also be hard to determine how many clades a specimen belongs to. Furthermore, clades intersect with Linnean taxonomy in varied and often inconsistent ways. Currently, many paleo collections are managing data about unranked clades eitey by shoehorning them into fields designed for Linnean taxonomy or into a notes field. Both of these options limit discoverability.
Identification qualifiersNotation that modifies a taxon name to reflect uncertainty (e.g. cf., aff., ?).–such as “cf.”, “aff.”, “sp. A,” “sp. etxc.”, etc.– are especially important in paleo collections. Figure 1 in Sigovini et al. 2016 offers a good framework for how to use qualifiers in taxonomy.
Resources for taxonomy
Higher taxonomy across fossil taxonomic groups
Useful for higher taxonomy. WoRMS is a dynamic database with many editors and daily updates. Some information is conflicting, and it includes unpublished taxonomic checklists for groups not critically evaluated in literature. Sometimes there is a lack of transparency in which publications/unpublished checklists are relied upon. This is a good source for taxonomic trees that overlap with extant groups.
Metadata record last updated on 2025-07-09
Useful for higher taxonomy, as well as some lower taxonomy for fossil plants, algae, fungi, cyanobacteria, pollen and spores and microfossils not listed in other databases. Classification for most groups is to genus level only.
Metadata record last updated on 2025-07-09
Useful for all taxonomic levels, although there are still many missing taxonomic classifications as well as conflicting information. Critically, taxonomic names in PBDB are transparently tied to published literature, and additionly linked to physical occurrences (geospatial, temporal, stratigraphic data).
Metadata record last updated on 2025-07-09
Can be useful for determining higher taxonomy, but not widespread in the paleo community.
Metadata record last updated on 2025-07-09
Can be useful for insects, though the focus is on modern species.
Metadata record last updated on 2025-07-09Micropaleontology
See Paleobotany (below) for pollen and spores.
Useful for looking up species level to higher taxonomy. Limited to foraminifera, including some not listed in other databases. Good images.
Metadata record last updated on 2025-07-09
Useful for higher taxonomy. WoRMS is a dynamic database with many editors and daily updates. Some information is conflicting, and it includes unpublished taxonomic checklists for groups not critically evaluated in literature. Sometimes there is a lack of transparency in which publications/unpublished checklists are relied upon. This is a good source for taxonomic trees that overlap with extant groups.
Metadata record last updated on 2025-07-09
Useful for higher taxonomy, as well as some lower taxonomy for fossil plants, algae, fungi, cyanobacteria, pollen and spores and microfossils not listed in other databases. Classification for most groups is to genus level only.
Metadata record last updated on 2025-07-09
Useful for all taxonomic levels, although there are still many missing taxonomic classifications as well as conflicting information. Critically, taxonomic names in PBDB are transparently tied to published literature, and additionly linked to physical occurrences (geospatial, temporal, stratigraphic data).
Metadata record last updated on 2025-07-09Ichnology/Trace fossils
K. Carpenter, K. F. Hirsch, J. R. Horner
Useful reference for the parataxonomy of fossil eggshells and the higher taxonomy of the possible eggshell maker.
Metadata record last updated on 2025-07-09Martin Lockley, Judy Peterson
Useful for determining ichnotaxonomy of fossil tracks and trackways, as well as the higher taxonomy of the possible track maker. This is a fairly general book, meant for a broad public audience rather than a scientific one. However, it does contain references to other manuscripts, which can then be used for deeper research.
Metadata record last updated on 2025-07-09
Useful for higher taxonomy, as well as some lower taxonomy for fossil plants, algae, fungi, cyanobacteria, pollen and spores and microfossils not listed in other databases. Classification for most groups is to genus level only.
Metadata record last updated on 2025-07-09
Useful for all taxonomic levels, although there are still many missing taxonomic classifications as well as conflicting information. Critically, taxonomic names in PBDB are transparently tied to published literature, and additionly linked to physical occurrences (geospatial, temporal, stratigraphic data).
Metadata record last updated on 2025-07-09Invertebrate paleontology
Multi-volume work that is useful for many taxonomic groups and convenient in its broad coverage. Taxonomy for some groups is getting out of date. Provides morphologic, taxonomic, systematic, stratigraphic, and biogeographic information/data on organisms comprising all the “invertebrate” phyla with a significant fossil record. Volumes can be downloaded in their entirety or as individual chapters.
Metadata record last updated on 2025-07-09P. Bouchet, J.P. Rocroi, et al.
Useful for higher taxonomy (down to genus) of bivalves, both fossil and modern.
Metadata record last updated on 2025-07-09P. Bouchet, J.P. Rocroi, et al.
Useful for higher taxonomy (down to genus) of gastropods, both fossil and modern.
Metadata record last updated on 2025-07-09Joseph G. Carter et al.
Useful reference for high taxonomy (down to subfamily) of bivalves. Comprehensive for the fossil record. Precursor to the Digital Treatise for Bivalvia.
Metadata record last updated on 2025-07-09Eugene V. Coan, Paul Valentich-Scott, Frank R. Bernard
Useful for the identification of Pliocene-Pleistocene marine bivalves from Arctic Alaska to Baja California.
Metadata record last updated on 2025-07-09Eugene V. Coan, Paul Valentich-Scott
Useful for the identification of Pliocene-Pleistocene marine bivalves from Baja California to Peru.
Houston Gem and Mineral Society
Useful for the identification of Western Interior Cretaceous mollusks down to species. Some higher taxonomy is outdated.
Metadata record last updated on 2025-07-09James A. Blake, Andrew L. Lissner
Useful for the identification of Pliocene-Pleistocene marine invertebrates from western North America, particularly groups (bryozoa, polychaetes, decapods) not well documented elsewhere, especially in fossil literature.
Metadata record last updated on 2025-07-09W. F. Ponder, David R. Lindberg, Juliet M. Ponder
Two volumes. Useful reference for mollusks, although books need to be purchased.
Metadata record last updated on 2025-07-09
Useful for higher taxonomy. WoRMS is a dynamic database with many editors and daily updates. Some information is conflicting, and it includes unpublished taxonomic checklists for groups not critically evaluated in literature. Sometimes there is a lack of transparency in which publications/unpublished checklists are relied upon. This is a good source for taxonomic trees that overlap with extant groups.
Metadata record last updated on 2025-07-09
Useful for higher taxonomy, as well as some lower taxonomy for fossil plants, algae, fungi, cyanobacteria, pollen and spores and microfossils not listed in other databases. Classification for most groups is to genus level only.
Metadata record last updated on 2025-07-09
Useful for all taxonomic levels, although there are still many missing taxonomic classifications as well as conflicting information. Critically, taxonomic names in PBDB are transparently tied to published literature, and additionly linked to physical occurrences (geospatial, temporal, stratigraphic data).
Metadata record last updated on 2025-07-09Paleobotany
Including palynology.
Literature-based record of the scientific names of all fossil plants, algae, fungi, allied prokaryotic forms, protists, and microproblematica. This resource aims to be comprehensive, but is also still actively growing and as such many taxonomic classifications are not captured yet.
Metadata record last updated on 2025-07-09
Scope is modern vascular plants, but higher taxonomy can be useful for fossil plant taxa.
Metadata record last updated on 2025-07-09
Multi-volume work published by the U.S. Geological Survey from 1820 to 2000. Useful for information about genus and taxa authorship.
Metadata record last updated on 2025-07-09
Multi-volume work published by the U.S. Geological Survey from 1820 to 2000. Useful for information about genus and taxa authorship.
Metadata record last updated on 2025-07-09
Multi-volume work published by the U.S. Geological Survey from 1820 to 2000. Useful for information about genus and taxa authorship.
Metadata record last updated on 2025-07-09
Multi-volume work published by the U.S. Geological Survey from 1820 to 2000. Useful for information about genus and taxa authorship. This volume is also known as Fossilium Catalogus II: Plantae, and does not appear to be digitally accessible.
Metadata record last updated on 2025-07-09Jansonius, Hills
Useful for information about genus and taxa authors of fossil pollen and spores. Compiled by Jansonius & Hills (1976–2002) and not somewhat outdated.
Metadata record last updated on 2025-07-09
Useful for information about diatoms, both extant and extinct.
Metadata record last updated on 2025-07-09
Comprehensive classification for bryophyte names. Includes hornworts, liverworts, and mosses. Focus is on modern taxa.
Metadata record last updated on 2025-07-09
Provides information on the current consensus on the fungal taxonomic hierarchy down to genus. Useful for yeasts, lichens, chromistan fungal analogues, protozoan fungal analogues and fossil forms at all ranks.
Metadata record last updated on 2025-07-09
Relevant for pteridophytes, both extinct and extant. Symbiota portal and associated taxonomic dictionary were orginally created for the Pteridophyte Thematic Collections Network.
Metadata record last updated on 2025-09-12
A consortium of natural history and botanical libraries that cooperate to digitize and make accessible the legacy literature of biodiversity held in their collections. BHL content may be freely viewed through the online reader or downloaded in part or as a complete work in PDF, OCR text, or JPG2000 file formats. Useful for finding historic taxonomic names in their original literature context.
Metadata record last updated on 2025-09-24
Useful for higher taxonomy. WoRMS is a dynamic database with many editors and daily updates. Some information is conflicting, and it includes unpublished taxonomic checklists for groups not critically evaluated in literature. Sometimes there is a lack of transparency in which publications/unpublished checklists are relied upon. This is a good source for taxonomic trees that overlap with extant groups.
Metadata record last updated on 2025-07-09
Useful for higher taxonomy, as well as some lower taxonomy for fossil plants, algae, fungi, cyanobacteria, pollen and spores and microfossils not listed in other databases. Classification for most groups is to genus level only.
Metadata record last updated on 2025-07-09
Useful for all taxonomic levels, although there are still many missing taxonomic classifications as well as conflicting information. Critically, taxonomic names in PBDB are transparently tied to published literature, and additionly linked to physical occurrences (geospatial, temporal, stratigraphic data).
Metadata record last updated on 2025-07-09
Can be useful for determining higher taxonomy, but not widespread in the paleo community.
Metadata record last updated on 2025-07-09Vertebrates
Malcom C. McKenna, Susan K. Bell
Useful for mammalian taxa above the species level. The book is now 20 years old though and is becoming a bit out of date.
Metadata record last updated on 2025-07-09Robert L. Carroll
Useful for vertebrate taxa above the species level, particularly as a standard for systematic organization of collections. Book is several decades old though, and becoming a bit out of date.
Metadata record last updated on 2025-07-09Hans-Dieter Sues
Useful for Reptilia higher classifications as it is the most recent major publication summarizing reptile taxonomy. Book does not go into great depth for dinosaur taxonomy, but is still a good overview. Has helpful classification table. No free digital version available.
Metadata record last updated on 2025-07-09Michael J. Benton
Useful for relatively up-to-date vertebrate higher taxonomy with coverage for all major taxa. Often used in vertebrate paleontology courses for its review of all vertebrate evolution.
Metadata record last updated on 2025-07-09T. S. Kemp
Useful for fossil mammalian taxonomy. Slightly out of date, but can be used in conjunction with other books/resources.
Metadata record last updated on 2025-07-09Christian F. Kammerer, Kenneth D. Angielczyk, Jorg Frobisch
Regarded as best source for Dicynodont taxnomy and synonyms.
Metadata record last updated on 2025-07-09Zofia Kielan-Jaworowska, Richard L. Cifelli, Zhe-Xi Luo
Useful for Mesozoic early mammal taxonomy.
Metadata record last updated on 2025-07-09Joseph S. Nelson, Terry C. Grande, Mark V. H. Wilson
Regarded as a good resource for fish taxonomy, including extinct taxa to at least the generic level.
Metadata record last updated on 2025-07-09Mikko Haaramo
Useful as an exploratory resource for higher taxonomy of all chordates.
Metadata record last updated on 2025-07-09https://cretaceousmadagascar.symbiota.org/portal/misc/contacts.php
Symbiota portal specific to a collaborative digitization project between the Denver Museum of Nature and Science and University of Antananarivo. Includes a curated taxonomic thesaurus.
Metadata record last updated on 2025-09-12
Information about species. Mostly for extant vertebrates but does include some extinct taxa.
Metadata record last updated on 2025-07-09
Useful for higher taxonomy. WoRMS is a dynamic database with many editors and daily updates. Some information is conflicting, and it includes unpublished taxonomic checklists for groups not critically evaluated in literature. Sometimes there is a lack of transparency in which publications/unpublished checklists are relied upon. This is a good source for taxonomic trees that overlap with extant groups.
Metadata record last updated on 2025-07-09
Useful for higher taxonomy, as well as some lower taxonomy for fossil plants, algae, fungi, cyanobacteria, pollen and spores and microfossils not listed in other databases. Classification for most groups is to genus level only.
Metadata record last updated on 2025-07-09
Useful for all taxonomic levels, although there are still many missing taxonomic classifications as well as conflicting information. Critically, taxonomic names in PBDB are transparently tied to published literature, and additionly linked to physical occurrences (geospatial, temporal, stratigraphic data).
Metadata record last updated on 2025-07-09Related content
- Catalogue of Life (Highlighted resource): This is a landing page that describes what the Catalogue of Life is and why it is important in the context of paleo data. You can dive deeper via the links to related resources aggregated here.
- Checklist Bank (Highlighted resource): This is a landing page that describes what Checklist Bank is and why it is important in the context of paleo data. You can dive deeper via the links to related resources aggregated here.
- Global Names Architecture (Highlighted resource): This is a landing page that describes what Global Names Architecture is and why it is important in the context of paleo data. You can dive deeper via the links to related resources aggregated here.
- PBot Integrative Paleobotany Portal (Highlighted resource): This is a landing page that describes what PBot is and why it is important in the context of paleo data. You can dive deeper via the links to related resources aggregated here.
- TaxonWorks (Highlighted resource): This is a landing page that describes what TaxonWorks is and why it is important in the context of paleo data. You can dive deeper via the links to related resources aggregated here.
- Treatise on Invertebrate Paleontology (Highlighted resource): This is a landing page that describes what the Treatise on Invertebrate Paleontology is and why it is important in the context of paleo data. You can dive deeper via the links to related resources aggregated here.
Browse additional related content, including PDWG Happy Hours and links out to external resources, via topic: taxonomy