Manage data about taxonomy
Draft: The content on this page has not been finalized. Contributors can mark a page as complete and remove this warning by adding status: published to the front matter in the Markdown source file.
Content to expand on
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 / synonyms (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 authority 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 WoRMS) for taxon concepts
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 ICZN (1999) recognizes “incertae sedis” but recommends attaching the highest known taxonomic level, e.g. “Cephalopoda incertae sedis.”
Unranked clades 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 qualifiers–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.
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.
Useful for higher taxonomy.
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).
Can be useful for determining higher taxonomy, but not widespread in the paleo community.
Can be useful for insects, though the focus is on modern species.
Micropaleontology
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.
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.
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.
Useful for higher taxonomy.
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).
Ichnology/Trace fossils
Useful reference for the parataxonomy of fossil eggshells and the higher taxonomy of the possible eggshell maker.
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.
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.
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).
Invertebrate 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.
Useful for higher taxonomy (down to genus) of bivalves, both fossil and modern.
Useful for higher taxonomy (down to genus) of gastropods, both fossil and modern.
Useful reference for high taxonomy (down to subfamily) of bivalves. Comprehensive for the fossil record. Precursor to the Digital Treatise for Bivalvia.
Useful for the identification of Pliocene-Pleistocene marine bivalves from Arctic Alaska to Baja California.
Useful for the identification of Pliocene-Pleistocene marine bivalves from Baja California to Peru.
Useful for the identification of Western Interior Cretaceous mollusks down to species. Some higher taxonomy is outdated.
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.
Two volumes. Useful reference for mollusks, although books need to be purchased.
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.
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.
Useful for higher taxonomy.
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).
Paleobotany
Including palynology.
Multi-volume work published by the U.S. Geological Survey from 1820 to 2000. Useful for information about genus and taxa authorship.
Multi-volume work published by the U.S. Geological Survey from 1820 to 2000. Useful for information about genus and taxa authorship.
Multi-volume work published by the U.S. Geological Survey from 1820 to 2000. Useful for information about genus and taxa authorship.
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.
Useful for information about genus and taxa authors of fossil pollen and spores. Compiled by Jansonius & Hills (1976–2002) and not somewhat outdated.
Useful for information about diatoms, both extant and extinct.
Comprehensive classification for bryophyte names. Includes hornworts, liverworts, and mosses. Focus is on modern taxa.
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.
Relevant for pteridophytes, both extinct and extant. Symbiota portal and associated taxonomic dictionary were orginally created for the Pteridophyte Thematic Collections Network.
Useful for locating historic taxonomic names not listed in other databases.
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.
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.
Useful for higher taxonomy.
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).
Can be useful for determining higher taxonomy, but not widespread in the paleo community.
Vertebrates
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.
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.
Useful for higher taxonomy.
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).
External resources
- AlgaeBase: Useful for information about diatoms, both extant and extinct.
- Open nomenclature:
- Vertebrate Palaeontology: 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.
- Biodiversity Heritage Library (BHL): Useful for locating historic taxonomic names not listed in other databases.
- Taxonomic atlas of the benthic fauna of the Santa Maria Basin and western Santa Barbara Channel: 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.
- Nomenclator of Bivalve Families with a Classification of Bivalve Families: Useful for higher taxonomy (down to genus) of bivalves, both fossil and modern.
- Revised Classification, Nomenclator and Typification of Gastropod and Monoplacophoran Families: Useful for higher taxonomy (down to genus) of gastropods, both fossil and modern.
- The Bryophyte Nomenclator: Comprehensive classification for bryophyte names. Includes hornworts, liverworts, and mosses. Focus is on modern taxa.
- BugGuide: Can be useful for insects, though the focus is on modern species.
- Dinosaur Eggs and Babies: Useful reference for the parataxonomy of fossil eggshells and the higher taxonomy of the possible eggshell maker.
- Vertebrate Paleontology and Evolution: 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.
- A Synoptical Classification of the Bivalvia (Mollusca): Useful reference for high taxonomy (down to subfamily) of bivalves. Comprehensive for the fossil record. Precursor to the Digital Treatise for Bivalvia.
- Bivalve seashells of western North America: Useful for the identification of Pliocene-Pleistocene marine bivalves from Arctic Alaska to Baja California.
- Bivalve seashells of tropical west America: Useful for the identification of Pliocene-Pleistocene marine bivalves from Baja California to Peru.
- Catalogue of Life: Useful for higher taxonomy.
- Foraminifera Database: Useful for looking up species level to higher taxonomy. Limited to foraminifera, including some not listed in other databases. Good images.
- Genera File of Fossil Spores: Useful for information about genus and taxa authors of fossil pollen and spores. Compiled by Jansonius & Hills (1976–2002) and not somewhat outdated.
- Index of generic names of fossil plants, 1820-1965: Multi-volume work published by the U.S. Geological Survey from 1820 to 2000. Useful for information about genus and taxa authorship.
- Index of generic names of fossil plants, 1966-1973: Multi-volume work published by the U.S. Geological Survey from 1820 to 2000. Useful for information about genus and taxa authorship.
- Index of generic names of fossil plants, 1974-1978: Multi-volume work published by the U.S. Geological Survey from 1820 to 2000. Useful for information about genus and taxa authorship.
- Index of generic names of fossil plants, 1979-2000: 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.
- Interim Register of Marine and Nonmarine Genera (IRMING): 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.
- Integrated Taxonomic Information System (ITIS): Can be useful for determining higher taxonomy, but not widespread in the paleo community.
- LACMIP EMu Handbook: EPICC Taxonomy: Guide designed to help staff and users of the LACMIP collections understand how the taxonomic dictionary created for a digitization project (EPICC) was migrated into the Taxonomy module in this institution's instance of EMu.
- LACMIP EMu Handbook: Taxonomy: Guide designed to help staff and users of the LACMIP collections navigate the Taxonomy module in this institution's instance of EMu.
- A Guide to the Fossil Footprints of the World: 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.
- Classification of Mammals Above the Species Level: Useful for mammalian taxa above the species level. The book is now 20 years old though and is becoming a bit out of date.
- Paleobiology Database (PBDB): 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).
- Plant Fossil Names: Useful for discovering names at all taxonomic levels. Includes mainly newer published names and older names mentioned in taxonomic discussions. There are still many missing taxonomic classifications.
- Biology and evolution of the mollusca: Two volumes. Useful reference for mollusks, although books need to be purchased.
- Pteridophyte Collections Consortium Taxonomic Dictionary: Relevant for pteridophytes, both extinct and extant. Symbiota portal and associated taxonomic dictionary were orginally created for the Pteridophyte Thematic Collections Network.
- Open Nomenclature in the biodiversity era: Includes useful framework for applying taxonomic qualifiers.
- Species Fungorum: 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.
- The Rise of Reptiles: 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.
- Texas Cretaceous series: Useful for the identification of Western Interior Cretaceous mollusks down to species. Some higher taxonomy is outdated.
- Treatise on Invertebrate 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.
- International Fossil Plant Names Index (IFPNI): 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.
- International Plant Names Index (IPNI): Scope is modern vascular plants, but higher taxonomy can be useful for fossil plant taxa.
- World Register of Marine Species (WoRMS): 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.