University of Glasgow

Roderic Page

I\'ve been thinking a bit about how one could use a Markdown wiki-like
tool such as Obsidian to work with taxonomic data (see earlier posts
[Obsidian, markdown, and taxonomic
trees](https://iphylo.blogspot.com/2022/04/obsidian-markdown-and-taxonomic-trees.html)
and [Personal knowledge graphs: Obsidian, Roam, Wikidata, and
Xanadu](https://iphylo.blogspot.com/2020/08/personal-knowledge-graphs-obsidian-roam.html)).

One \"gotcha\" would be how to name pages. If we treat the database as
entirely local, then the page names don\'t matter, but what if we
envisage sharing the database, or merging it with others (for example,
if we divided a taxon up into chunks, and different people worked on
those different chunks)?

This is the attraction of globally unique identifiers. You and I can
independently work on the same thing, such as data linked to scientific
paper, safe in the knowledge that if we both use the DOI for that paper
we can easily combine what we\'ve done. But global identifiers can also
be a pain, especially if we need to use a service to look them up (\"is
there a DOI for this paper?\", \"what is the LSID for this taxonomic
name?\").

Life would be easier if we could generate identifiers \"locally\", but
had some assurance that they would be globally unique, and that anyone
else generating an identifier for the same thing would arrive at the
same identifier (this eliminates things such as
[UUIDs](https://en.wikipedia.org/wiki/Universally_unique_identifier)
which are intentionally designed to prvent people genrrating the same
identifier). One approach is \"content addressing\" (see, e.g.
[Principles of Content
Addressing](https://web.archive.org/web/20210514054054/https://bentrask.com/notes/content-addressing.html) -
dead link but in the Wayabck Machine, see also
[btrask/stronglink](https://github.com/btrask/stronglink)). For example,
we can generate a cryptographic hash of a file (such as a PDF) and use
that as the identifier.

Now the problem is that we have globally unique, but ugly and unfriendly
identifiers (such as \"6c98136eba9084ea9a5fc0b7693fed8648014505\"). What
we need are nice, easy to use identifiers we can use as page names.
[Wikispecies](https://species.wikimedia.org/wiki/Main_Page) serves as a
possible role model, where taxon names serve as page names, as do
simplified citations (e.g., authors and years). This model runs into the
problem that taxon names aren\'t unique, nor are author + year
combinations. In Wikispecies this is resolved by having a centralised
database where it\'s first come, first served. If there is a name clash
you have to create a new name for your page. This works, but what if you
have multiple databases un by different people? How do we ensure the
identifiers are the same?

Then I remembered Roger Hyam\'s flight of fantasy over a decade ago:
[SpeciesIndex.org -- an impractical, practical
solution](http://www.hyam.net/blog/archives/1007). He proposed the
following rules to generate a unique URI for a taxonomic name:

- The URI must start with \"http://speciesindex.org\" followed by one or
  more of the following separated by slashes.
- First word of name. Must only contain letters. Must not be the same as
  one of the names of the nomenclatural codes (icbn or iczn). Optional
  but highly recommended.
- Second word of name. Must only contain letters and not be a
  nomenclatural code name. Optional.
- Third word of name. Must only contain letters and not be a
  nomenclatural code name. Optional.
- Year of publication. Must be an integer greater than 1650 and equal to
  or less than the current year. If this is an ICZN name then this
  should be the year the species (epithet) was published as is commonly
  cited after the name. If this is an ICBN name at species or below then
  it is the date of the combination. Optional. Recommended for
  zoological names if known. Not recommended for botanical names unless
  there is a known problem with homonyms in use by non-taxonomists.
- Nomenclatural code governing the name of the taxon. Currently this
  must be either \'icbn\' or \'iczn\'. This may be omitted if the code
  is unknown or not relevant. Other codes may be added to this list.
- Qualifier This must be a Version 4 RFC-4122 UUID. Optional. Used to
  generate a new independent identifier for a taxon for which the
  conventional name is unknown or does not exist or to indicate a
  particular taxon concept that bears the embedded name.
- The whole speciesindex.org URI string should be considered case
  sensitive. Everything should be lower case apart from the first letter
  of words that are specified as having upper case in their relevant
  codes e.g. names at and above the rank of genus.

Roger is basically arging that while names aren\'t unique (i.e., we have
homonyms such as *Abronia*) they are pretty close to being so, and with
a few tweaks we can come up with a unique representation. Another way to
think about this if we had a database of all taxonomics, we could
construct a [trie](https://en.wikipedia.org/wiki/Trie) and for each name
find the shortest set of name parts (genus, species, etc), year, and
code that gave us a unique string for that name. In many cases the
species name may be all we need, in other cases we may need to add year
and/or nomenclatural code to arrive at a unique string.

What about bibliographic references? Well many of us will have databases
(e.g., Endnote, Mendeley, Zotero, etc.) which generate \"cite keys\".
These are typically short, memorable identifiers for a reference that
are unique within that database. There is an interesting discussion on
the [JabRef
forum](https://discourse.jabref.org/t/universal-citekey-generator/2441/2)
regarding a \"Universal Citekey Generator\", and source code is
available
[cparnot/universal-citekey-js](https://github.com/cparnot/universal-citekey-js).
I\'ve yet to explore this in detail, but it looks a promising way to
generate unique identifiers from basic metadata (echos of more elaborate
schemes such as
[SICIs](https://en.wikipedia.org/wiki/Serial_Item_and_Contribution_Identifier)).
For example,

> Senna AR, Guedes UN, Andrade LF, Pereira-Filho GH. 2021. A new species
> of amphipod Pariphinotus Kunkel, 1910 (Amphipoda: Phliantidae) from
> Southwestern Atlantic. Zool Stud 60:57. doi:10.6620/ZS.2021.60-57.

becomes \"Senna:2021ck\". So if two people have the same, core, metadata
for a paper they can generate the same key.

Hence it seems with a few conventions (and maybe some simple tools to
support them) we could have decentralised wiki-like tools that used the
same identifiers for the same things, and yet those identfiiers were
short and human-friendly.


I've been thinking a bit about how one could use a Markdown wiki-like tool such as Obsidian to work with taxonomic data (see earlier posts Obsidian, markdown, and taxonomic trees and Personal knowledge graphs: Obsidian, Roam, Wikidata, and Xanadu).  One "gotcha" would be how to name pages.

Messaggi di Rogue Scholar

Local global identifiers for decentralised wikis