species-brainstorming
Species Brainstorming
- Note: the original name of the proposed microformat, "species", is likely to change, probably to "biota" or "taxon". The former has been retained here, to avoid having to make many repetitive and perhaps redundant edits
Andy Mabbett
Proposal
There should, I believe, be a "species" microformat for the markup of plant and animal names, to include their scientific names. Consider:
<abbr class="species" title="Anas platyrhynchos">Mallard</abbr>
or
<span class="species">Anas platyrhynchos</span>
The microformat would allow user agents to be configured to perform look-ups on on-line databases of species, according to user preferences. Specification of the taxonomic class would help user agents to know which such databases were applicable (i.e., use database A for plants, but database B for mammals and database C for insects.)
It would also allow for more specific searching (do I mean "crow" or do I mean "Corvus corone"?).
The specification should encourage, but not mandate, the correct capitalisation of scientific names, so "Anas platyrhynchos'" not "anas platyrhynchos" nor (except historically) "Anas Platyrhynchos". A reminder that such names should be styled with italics will also be included.
Straw man proposal
I'm tending towards this model, nested according to components of the microforamt, not taxonomically:
[Note: in taxonomy, levels such as "subphylum", "class" or "order" are known as a "rank"].
- species (scientific name; aka botanical name) (better: taxon; or biota)
- domain (alternatively: "superregnum")
- kingdom (alt: "regnum")
- subkingdom (alt: "subregnum")
- superphylum
- phylum
- subphylum
- taxoclass (alt: "taxo-class ", "taxonclass", "taxon-class", "classis")
- subclass (alt: "subclassis")
- infraclass (alt: "infraclassis")
- superorder (alt: "superordo")
- order (alt: "ordo")
- suborder (alt: "subordo")
- infraorder (alt: "infraordo")
- parvorder
- superfamily (alt: "superfamilia")
- family (alt: "familia")
- subfamily (alt: "subfamilia")
- rank (alt: "taxorank", "taxon-rank", et al) - "unranked". See [1]; might also be used where the level of a rank is disputed, or the author simply has no ability or wish to declare the rank more explicitly.
- binominal ("binominal name" alt: "binomial")
- genus
- specific (="specific epithet")
- subsp ("subspecies")
- variety
- subvar ("subvariety")
- form
- subform
- cultivar
- cultgp ("cultivar group")
- cross (e.g. "F1")
- strain
- ? morph (or phase) (e.g "Gyrfalcons, for example, have a grey morph and a white morph" [2]; "the Lesser Snow Goose (C. c. caerulescens), commonly occurs in two plumage variants. White-phase birds are white except for black wing tips, but blue-phase geese have bluish-grey plumage replacing most of the white except on the head, neck and tail tip." [3])
- trade ("trade name")
- breed (e.g. Bull Terrier)
- sense (botanical - see examples)
- authority
- year (...of authority)
- cname ("common name" - should this be "common" or "vernacular"?)
- guid
- vgroup ("vernacular group" (alt: "vernacular-group") - there is possibly a better term for this. Often, a genus or family doesn't encapsulate a particular group of species in a practical or useful fashion. For example, it is difficult to seperate fungi species and lichen species as they are taxonomically intermingled. Thus, within taxonomic databases, a vernacular group of "fungi" and "lichen" is often applied to species falling into either of these groups. A vernacular group could be considered similar to a common name, but for groups of species. See the NBN Gateway for an example of vernacular groups in use; these group names are also used in the Recorder biological recording software.
- ? gender (useful for species exhibiting sexual dimorphism - "find me a picture of a male Pintail"; "I want to buy a female Holly bush" - a binary value, male or female; or including nueter, hermaphoradite, unspecified and/ or mixed?)- see Future development
- ? age bracket (adult/ juvenile/ seed/ egg/ nymph/ nestling/ pup/ cub/ instar1/ instar2 etc. - needs more work) - see Future development
- ? count (a number, or represenattion of some other value - none, unspecified, "present", etc) - see Future development
- [name to be suggested ("type", "role"?)] an indicator of type, e.g. for bees, "queen" or "worker" [Q: Is there a proper name, in the scientific cmmnuity, for thes edistinctions?]
where are optional, and it is possible to infer from simply:
<abbr class="binominal" title="Anas platyrhynchos">Mallard</abbr>
or
<span class="binominal">Anas platyrhynchos</span>
that the genus is Anas and the species is platyrhynchos (and, thus, "binominal" is to "sci"; as "adr" is to "hCard")
Examples
Extreme case (Pied Wagtail, a bird):
<span class="species">
<span class="domain">Eukarya</span>
<span class="kingdom">Animalia</span>
<span class="subkingdom">Eumetazoa</span>
<span class="superphylum">Deuterostomia</span>
<span class="phylum">Chordata</span>
<span class="subphylum">Vertebrata</span>
<span class="taxoclass">Aves</span>
<span class="subclass">Neognathae</span>
<span class="order">Passeriformes</span>
<span class="suborder">Passeri</span>
<span class="parvordo">Passerida</span>
<span class="superfamily">Passeroidea</span>
<span class="family">Motacillidae</span>
<span class="binominal">
<span class="genus">Motacilla</span>
<span class="specific">alba</span>
<span class="subspecies">yarrellii</span>
</span>
<span class="cname">Pied Wagtail</span>
<span class="authority">Linnaeus</span>
<span class="year">1758</span>
</span>
Simplified equivalent of the above:
<span class="species">
<span class="binominal">Motacilla alba</span>
<span class="subspecies">yarrellii</span>
</span>
Sub-species (animal, common name displayed):
<span class="species">
<span class="binominal">Larus glaucoides</span>
<span class="subsp">kumlieni</span>
</span>
Variety (plant):
<span class="species">
<span class="binominal">Pisum sativum</span>
var. <span class="variety">macrocarpon</span>
</span>
Species (animal, common name displayed):
<span class="species">
<abbr class="binominal" title="Larus thayeri">
<span class="common">Thayer's Gull</span>
</abbr>
</span>
Species (animal, scientific name displayed):
<span class="species">
<abbr class="common" title="Thayer's Gull">
<span class="binominal" Larus thayeri</span>
</abbr>
</span>
Fungus, kingdom included:
<span class="species">
<abbr class="kingdom" title="Fungi">
<span class="binominal">Amanita muscaria</span>
</abbr>
</span>
Same name for different Genera:
<p class="species">
An unidentified
<abbr class="taxoclass" title="Aves">
<abbr class="genus" title="Oenanthe">
<span class="common">
Wheatear
</span>
</abbr>
</abbr>
</p>
and :
<p class="species">
An unidentified
<abbr class="taxoclass" title="Magnoliopsida">
<abbr class="genus" title="Oenanthe">
<span class="common">
Water Dropwort
</span>
</abbr>
</abbr>
sp.
</p>
Species (animal, with authority and year):
<span class="species">
<span class="binominal">Pica pica</span>
<span class="authority">Linnaeus</span>,
(<span class="year">1758</span>)
</span>
Re-classified species (animal):
The species was classified as
<span class="species">
<abbr class="binominal" title="Bartramia longicauda">Tringa longicauda</abbr>
by Johann Bechstein in 1812.
</span>
Expressing a species with a GUID
Work is currently underway, through TDWG to develop a truly global GUID system based on LSIDs. More on LSIDs.
In the following example case an NBN GUID is provided. This GUID would be usable on the NBN Gateway, The NHM Species Dictionary, in Recorder 2002 and Recorder 6, and in the forthcoming OpenRecorder online recording toolkit. As there are different GUIDs for different databases, the type of GUID can be indicated with a code followed by a hyphen followed by the GUID (e.g. nbn-NBNSYS0000005133).
<span class="sci nbn-NBNSYS0000005133">
<span class="binominal">Lutra lutra</span>
</span>
Alternatively, the GUID could be expressed as an element in its own right, with the GUID type being expressed as a secondary class name:
<span class="species">
<span class="binominal">Lutra lutra</span>
<span class="uid nbn">NBNSYS0000005133</span>
</span>
As a further alternative, the abbr-design-pattern could potentially be used, although this is semantically questionable:
<span class="species">
<abbr class="binominal" title="NBNSYS0000005133">Lutra lutra</abbr>
</span>
Yet another alternative, using a uBio LSID as the GUID:
<span class="species urn:lsid:ubio.org:namebank:8341384">
<span class="cname">Green Sandpiper</span>
<span class="binominal">Tringa ochropus</span>
</span>
uBio has a publicly available SOAP web services interface which makes mining for taxonomic intelligence relatively easy.
Questions
- Is "sci" the best attribute name for the top-level?
- No - Scott Reynen
- What do you think would be better? - Andy Mabbett
- Assuming "sci" is short for "scientific name", I propose "scientific-name".
- It is. That's 12 extra characters! - Andy Mabbett
- Assuming "sci" is short for "scientific name", I propose "scientific-name".
- What do you think would be better? - Andy Mabbett
- Taxon is a far better solution [4]. It's short, meaningful and in keeping with the other class types. - Andy Mabbett
- I think "taxonname" or "taxon-name" would be a better value for the class attribute. It is more descriptive of the data your trying to specify the format of. Taxon refers more to the classification grouping I thought. The class attribute is used frequently for the application of CSS styling so the top level class at least needs to be fairly distinctive I would have thought to avoid clashes with other class attribute values in the page and CSS files. - Tony Prichard
- or Biota - Andy Mabbett
- No - Scott Reynen
- Species is used in the above, for the sake of having one name to use, but "biota" or "taxon" are likely to be used in the final version. AndyMabbett 09:15, 22 Oct 2006 (PDT)
- Should "bin", var", "cult", etc., be written in full? (I think not, to save bloating file sizes)
- Yes - Scott Reynen
- Conceded, and applied to the above. What about "subsp", etc? AndyMabbett 09:15, 22 Oct 2006 (PDT)
- Yes - Scott Reynen
- Should other attribute names be abbreviated for brevity?
- No, brevity is not one of the naming principles. "bin", "var", and "cult" all leave ambiguous meaning, which is a problem. We should "Use class names based on names from the original schema," e.g. full words or phrases where they aren't especially long. - Scott Reynen
- Fair enough, though I worry about some of my pages, with tens or hundreds of species listed! Also, note that "var" "sub" and suchlike are the proper abbreviations to use, in botanical nomenclature (see the posted examples). - Andy Mabbett
- I think a balance will need to be achieved between brevity in the interests of avoiding bloated html in a page with many species names and giving a meaningful name - Tony Prichard
- Would bloating really be an issue? Many, if not most, servers (including this one) now gzip,deflate content and thus transfer time aren't so much of an issue. The front page of the microformats site states "Designed for humans first and machines second[...]", so unabbreviated terms would be more consistent with this aim. - Charles Roper
- 341 species, 58Kb. 'Nuff said? AndyMabbett 11:53, 26 Sep 2006 (PDT)
- Your bird list page can be compressed by 79%, i.e. it would go down from 58KB to 12KB by enabling output compression on your server. It would also make the page load faster and save you bandwidth. No doubt compression technologies will improve over time, as will connection speeds and server speeds, so the technical solution to reducing page size would seem to me to be preferable over the "manual compression" method, i.e. using abbreviated, less clear, less readable class names. While it is easy to improve the compression technology (or switch it on, even), it's much harder to change an established microformat standard. - Charles Roper
- 341 species, 58Kb. 'Nuff said? AndyMabbett 11:53, 26 Sep 2006 (PDT)
- Would bloating really be an issue? Many, if not most, servers (including this one) now gzip,deflate content and thus transfer time aren't so much of an issue. The front page of the microformats site states "Designed for humans first and machines second[...]", so unabbreviated terms would be more consistent with this aim. - Charles Roper
- No, brevity is not one of the naming principles. "bin", "var", and "cult" all leave ambiguous meaning, which is a problem. We should "Use class names based on names from the original schema," e.g. full words or phrases where they aren't especially long. - Scott Reynen
- Is "class" a potentially confusing attribute name, and what should replace it ("taxoclass", perhaps? or "classis"?)
- Yes I would avoid class as it a frequent keyword in software languages - Tony Prichard
- "bin" and "var" are also extremely common terms using in programming languages - Charles Roper
- Conceded, and "taxoclass" applied to the above. "classis" would be an alternative. AndyMabbett 09:15, 22 Oct 2006 (PDT)
- Yes I would avoid class as it a frequent keyword in software languages - Tony Prichard
- What other attribute names are needed, if any (we could do with help from a taxonomist!)
- How to deal with: "Podiceps sp." (a grebe of unknown species)
- How about the following, where we can infer an unknown species by the absence of that attribute?:
<span class="bin"><span class="genus">Podiceps</span></span>
- There are also species aggregates and groups to be considered Grey/Dark Dagger sp., where it is one of two species but where the genus Acronicta cannot be used as there are more than the two species in the genus - Tony Prichard
- Any suggestions? Or other examples? - AndyMabbett
- This kind of aggregates are often used by birdwatchers (in Finland). How about separating the names with a slash (or some other sign)?: - MikkoBiomi
- Any suggestions? Or other examples? - AndyMabbett
- There are also species aggregates and groups to be considered Grey/Dark Dagger sp., where it is one of two species but where the genus Acronicta cannot be used as there are more than the two species in the genus - Tony Prichard
<span class="bin">Phylloscopus trochilus/Phylloscopus collybita</span>
<span class="bin"><span class="genus">Anser</span>/<span class="genus">Branta</span></span>
- Should we allow divisions of "binominal" with no parent "species", such as:
<span class="binominal">Larus glaucoides <span class="sub">kumlieni</span></span>
- Is the "fungus" example OK, given that Amanita muscaria is not an abbreviation of "funghi"?
- I do not like the use of the abbr tag at all in the examples given. The abbr tag is for abbreviations with the suggestion that the title is used for the full name. The implication in the Mallard example is that Mallard is an abbreviation for the scientific name, it is not it is a different type of name - Tony Prichard
- Do the "authority" and "date" pair need a joint wrapper?
- Is "bin" (short for binominal) the most appropriate term for a taxon name? When subspecies, var, subvar, etc. are nested, then surely it becomes trinomial? Would simply name or TaxonName not be more flexible? - Charles Roper
To add
- Animal hybrids
- GUID (Globally Unique Identifier). When referencing to a taxon name, there is also often the need to provide a GUID which relates to a taxonomic concept database (such as the NHM Species Dictionary). By providing a GUID, ambiguity is removed. - Charles Roper
- Thank you. AndyMabbett 11:55, 26 Sep 2006 (PDT)
Future development
Instead of including gender, age-bracket and count, we could allow for a furture microformat, called, perhpas, "sighting", which might have the components:
- sighting
- species (a "species" microformat)
- set (one or more)
- count
- age-bracket
- gender
- set (one or more)
- location (hCard or geo)
- date-time
- species (a "species" microformat)
See West Midland Bird Club's Latest news from Ladywalk and In and around South Staffordshire 2006 (blog) for simple examples.
Bill Hull
My website has 17000+ photos of 4700+ bird species. There are also a handful of butterflies (organized very poorly as I am unaware of any published butterfly world taxonomies) and shortly will have a number of dragon/damselflies. The site is made up of static pages but is built from a database so it is easy for me to add it new HTML tags to the pages. If you are interested in some prototyping at some point I can probably build stuff into the pages. - Bill Hull
Roger Hyam
Taxonomic Databases Working Group
TDWG is the organisation for standardisation in exchange of biodiversity data. The organisation is currently undergoing a degree of re-organisation and is developing an architecture to integrate the different standards it produces with each other and with those in use in the semantic web and geospatial communities. Part of this architecture will be a central ontology for things like scientific biological names.
Because of its role in bridging technologies the application that manages the ontology will need to be able to express the same basic semantics in multiple formats (e.g. RDFS, OWL, Geography Mark Up, OBO etc). It seems logical that this application should also generate basic microformat definitions for each of the classes it contains. If we have an ontology defining 'Taxon Name' and 'specific epithet' for example the same notion should be mapped to as many technologies as possible.
TDWG is also supporting a system for Globally Unique Identifiers based on Life Science Identifiers for biodiveristy objects such as taxon names, specimens, herbaria etc which it would be cool to integrate into any microformat.
There is a meeting in St Louis, USA, October 2006 where the way forward for the ontology will be discussed. Decisions made at the meeting will govern what is possible. It is difficult to take this further without concensus from that meeting.
If it is after October 2006 and you are interested in learning more please contact me (Roger Hyam).
- Thanks, Roger - it's good to have the involvement of such an august body, especially just before such a fortuitously-scheduled event. Is there any chance (and I realise that this is rather late in the day) that this proposal could be on the agenda in St Louis (even if only through a note in the papers/ programme); or that someone from the microformat community could attend/ speak there? Or that the TDWG and/or conference websites could link to http://microformats.org/wiki/species? - Andy Mabbett
Malcolm Storey
(extracted from e-mails to Andy Mabbett, by kind permission)
- "Hopefully I'll have more time for things like this in the New Year, but expect it all be done and dusted by then!!" - Malcolm Storey, BioImages
ICZN, ICBN et al
You don't cover the full set of levels of taxonomic hierarchy defined by the relevant body ICZN or ICBN (plus the others - one each for garden plant varieties, bacteria, viruses. Don't know about mycoplasmas, diseases, BSE factors etc.
AIUI ICBN only goes down to species.
ICZN isn't so easy: [8]
- 1.2.2. The Code regulates the names of taxa in the family group, genus group, and species group. Articles 1-4, 7-10, 11.1-11.3, 14, 27, 28 and 32.5.2.5 also regulate names of taxa at ranks above the family group. (But none of the above articles list the taxonomic ranks.)
ICZN Only goes down to subspecies (art 1.3.4)
Note also:
- 1.4. Independence. Zoological nomenclature is independent of other systems of nomenclature in that the name of an animal taxon is not to be rejected merely because it is identical with the name of a taxon that is not animal (see Article 1.1.1)
(eg Trichia, Oenanthe, Melanotus)
Myxomycetes are the exception - they're in kingdom protozoa which falls under ICZN but they fall under the ICBN name space. (Hence "Trichia").
DNA
You may want to consider refs to DNA sequences. They're not part of taxonomy, but they can be considered the bottom rung of the taxonomic hierarchy and they will be of increasing significance.
Typography
what about Adalia 2-punctata, and Adalia bipunctata (not to mention those with hyphens [or apostrophes] which may get left out. And what about accented characters)?
- Adalia 2-punctata is an abbreviation of Adalia bipunctata, so:
<abbr class="binominal" title="Adalia bipunctata">Adalia 2-punctata</abbr>
AndyMabbett 09:55, 21 Oct 2006 (PDT)
Gaps
The hierarchy is not always fully populated. Not every species belongs to a class. Maybe this was where fungi are different. In Paul Kirk's databases (which are the official ones used to drive the checklists and NBN) he has fixed fields for the higher level taxa which means that only certain ranks can be used. The blanks he fills in (mostly!!) with "insertae sedis" (think it's Latin for "unknown seat"). In my database I use a self-join which gives much more flexibility. Anyway there are lots of "insertae sedis" in Paul's database!
Homonyms
Apion carduorum sensu Morris 1990 is Apion gibbirostre (Gyllenhal, 1813). Apion carduorum Kirby, 1808 is a different species.
- You'd mark the former up as something like
<abbr class="binominal" title="Apion gibbirostre">''Apion carduorum'' sensu Morris 1990</abbr>
- AndyMabbett 12:21, 5 Oct 2006 (PDT)
Citations for authorites
If people are citing the authority in full they would include the literature reference, not just the date e.g.
- Cuphophyllus niveus (Scop.) Bon, Doc. Mycol. 14(56): 11 (1985)[1984]
Hyppo
Nomenclatural challenge
You asked for comments. One challenge I see is the difference in Nomenclature for Animalia and Plantae (coming from the old 2 kingdom system). For Plantae the International Code of Botanical Nomenclature[9] is used and for Animalia the code from http://www.iczn.org/. Animalia code is not officially accepted but ICZN tries to be authoritive starting from 2008.
The two different nomenclatural systems differ in a few areas, and they affect markup.
- Subgenus (Plantae): Dendroceros subg. Apoceros
- Subgenus (Animalia): Sula (Morus)
- Subspecies (Plantae): Begonia grandis ssp. evansiana
- Subspecies (Animalia): Gorilla beringei graueri
- --Hyppo 14:23, 9 Oct 2006 (PDT)
- I would mark those up as:
<span class=genus">Dendroceros</span> subg. <span class="subgenus">Apoceros</span>
<span class=genus">Sula</span> <span class="subgenus">Morus</span>
<span class="binominal">Begonia grandis</span> ssp. <span class="subspecies">evansiana''</span>
<span class="binominal">Gorilla beringei</span> <span class="subspecies">graueri</span>
- With wrapping class="biota" and possibly kingdom, attributes.
- AndyMabbett 11:37, 10 Oct 2006 (PDT)
Cyndy Parr
The ideas expressed here are promising. Below are my comments on all the preceding -- as I have time I'll organize, elaborate, and try to move parts into the right discussion threads above.
In the Spire project we have been developing ontologies in OWL for taxonomic names and hierarchies. Ideally, we'd like to have a microformat where people can tag a scientific name and an application can then check an ontology of their choice for more information (richer semantics).
We would discourage full expression of the Linnaean hierarchy except for those who are maintaining such classifications (such as uBio). The rest of the hierarchy can be retrieved ontologically as necessary.
Better to tie the scientific name (taxon name) to the authority or ontology from which it came. I.e. for those who are able to provide information on taxonomic concepts, support for TCS (Taxonomic Concept Schema) fields would be important.
I prefer "taxon" or "taxon-name" or TaxonName over biota (which is plural, and too close to biotic which has a far larger scope than taxa). Would prefer "binomial" to "binominal"
"class" is difficult not only because of the confusion with the programming concept of classes, but because it is a taxonomic rank. However, most of us have figured out the difference by now so this is not critical.
"cname" should be "comname" or "common-name" or "vernacular" to make it more obvious what the information is. A sub-component would be the language for which that common name is used ( something like an HTML attribute lang="en")
There are known conflicts between names across kingdoms (as current codes of nomenclature allow these). Thus specification of kingdom may be encouraged. Disambiguation could be handled by applications outside the microformats (this could be difficult), or they could be dealt with in the core microformat: e.g. plant-taxon or fungal-taxon or animal-taxon.
A sightings microformat is a good idea and I would be interested in being involved in that. We've been toying with this in OWL and also using structured blogging over at http://fieldmarking.reger.com
Your terms such as gender (better: sex), age bracket (better: life stage), count, type (better: depending on the meaning, caste or morph) all belong in a specimen or sighting microformat and used in combination with the taxon microformat, not be part of it.
Response by Andy Mabbett
Thank you very much for your detailed contribution. I have a few responses:
- We would discourage full expression of the Linnaean hierarchy except for those who are maintaining such classifications (such as uBio).
- Why? Also, I'm not aware of any microformat which is restricted to a subset of users, nor how this would be done. How would you suggest that someone mark up this: "Not all of the Passeriformes sing"?
- The rest of the hierarchy can be retrieved ontologically as necessary.
- That's a use-case once the uF is published, certainly. the proposal doesn't require that the hierarchy be marked-up, it merely allows for it, in cases where it is already published.
- Better to tie the scientific name (taxon name) to the authority or ontology from which it came.
- That would require the publisher to add extra data, which they might not wish to publish, nor, indeed, have to hand. Microformats are about recognising what data is already published and then enabling people to add semantics which identify the type of data on their pages.
- [common names] A sub-component would be the language for which that common name is used (something like an HTML attribute lang="en")
- Indeed, but that's already available, and (on properly constructed pages) should already be on the parent container.
- conflicts between names across kingdoms (as current codes of nomenclature allow these). Thus specification of kingdom may be encouraged.
- already in the proposal!
- Disambiguation could be handled by applications outside the microformats
- Not sure what you mean here, since all parsing is done "outside microformats".
(I'm either in agreement with your other points, or ambivalent.)
Thank you again - do stick around. Are you on the mailing list?
Andy Mabbett 11:06, 5 Jan 2007 (PST)
See also
- species
- examples
- quantitative evidence
- brainstorming (includes the straw man- or draft standard)