Local global identifiers for decentralised wikis

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. 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 which are intentionally designed to prvent people genrrating the same identifier). One approach is "content addressing" (see, e.g. Principles of Content Addressing - dead link but in the Wayabck Machine, see also 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 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. 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 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 regarding a "Universal Citekey Generator", and source code is available 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). 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.

Obsidian, markdown, and taxonomic trees

Returning to the subject of personal knowledge graphs Kyle Scheer has an interesting repository of Markdown files that describe academic disciplines at https://github.com/kyletscheer/academic-disciplines (see his blog post for more background).

If you add these files to Obsidian you get a nice visualisation of a taxonomy of academic disciplines. The applications of this to biological taxonomy seem obvious, especially as a tool like Obsidian enables all sorts of interesting links to be added (e.g., we could add links to the taxonomic research behind each node in the taxonomic tree, the people doing that research, etc. - although that would mean we'd no longer have a simple tree).

The more I look at these sort of simple Markdown-based tools the more I wonder whether we could make more use of them to create simple but persistent databases. Text files seem the most stable, long-lived digital format around, maybe this would be a way to minimise the inevitable obsolescence of database and server software. Time for some experiments I feel... can we take a taxonomic group, such as mammals, and create a richly connected database purely in Markdown?

Personal knowledge graphs: Obsidian, Roam, Wikidata, and Xanadu

The workflow & cost of my current Personal Knowledge OS setup, key tools includes @RoamResearch @readwiseio @instapaper @AirrAudio @reeder @evernote @obsdmd @SubstackInc @Medium

Current Per Month Total Cost: $48.83 pic.twitter.com/FtUy87zLFO

— Zack Fan (@zackfan01) August 25, 2020

I stumbled across this tweet yesterday (no doubt when I should have been doing other things), and disappeared down a rabbit hole. Emerging, I think the trip was worth it.

 

Markdown wikis

Among the tools listed by @zackfan01 were Obsidian and Roam, neither of which I heard of before. Both Obsidian and Roam are pitched as "note-taking" apps, they are essentially personal wikis where you write text in Markdown and use [[some text goes here]] to create links to other pages (very like a Wiki). Both highlight backlinks, that is, clearly displaying "what links here" on each page, making it easy to navigate around the graph you are creating by linking pages. Users of Obsidian share these graphs in Discord, rather like something from Martin MacInnes' novel "Gathering Evidence". Personal wikis have been around for a long time, but these apps are elegantly designed and seem fun to use. Looking at these apps I'm reminded of my earlier post Notes on collections, knowledge graphs, and Semantic Web browsers where I moaned about the lack of personal knowledge graphs that supported inference from linked data. I'm also reminded of the Blue Planet II, the BBC, and the Semantic Web: a tale of lessons forgotten and opportunities lost where I constructed an interactive tool to navigate BBC data on species and their ecology (you can see this live at https://rdmpage.github.io/bbc-wildlife/www/), and the fun to be had from simply being able to navigate around a rich set of links. I imagine these Markdown-based wikis could be a great way further explore these ideas.

 

Personal and global knowledge graphs

Then I began thinking about what if the [[page links]] in these personal knowledge graphs were not just some text but, say, a Wikidata identifier (of the form "Qxxxxx")? Imagine that if you were writing notes on say, a species, you could insert the Wikidata Qid and you would get a pre-populated template that comes with some facts from Wikidata, and you could then use that as a starting point (see for example Toby Hudson Entity Explosion I discussed earlier). Knowing that more and more scholarly papers are being added to Wikidata, this means you could also add bibliographic citations as Qids, fetching all the necessary bibliographic information on the fly from Wikidata. So your personal knowledge graph intersects with the global graph.

 

Roam

Now, I've not used Roam, but anyone who has is likely to balk at my characterisation of it as "just" a Markdown wiki, because there's more going on here. The Roam white paper talks about making inferences from the text using reasoning or belief networks, although these features don't seem to have had much uptake. But what really struck me as I explored Roam was the notion of not just linking to pages using the [[ ]] syntax, but also linking to parts of pages (blocks) using (( )). In the demo of Roam there are various essays, such as Paul Graham's The Refragmentation, and each paragraph is an addressable block that can be cited independently of the entire essay. Likewise, you can see what pages cite that block.

 Now in a sense these are just like fragment identifiers that we can use to link to parts of a web page, but there's something more here because these fragments are not just locations in a bigger document, they are the components of the document.

Xanadu

This strikes me as rather like Ted Nelson's vision of Xanadu, where you could cite any text at any level of granularity, and that text would be incorporated into the document you were creating via transclusion (i.e., you don't include a copy of the text, you include the actual text). In the context of Roam, this means you have the entire text you want to cite included in the system, so you can then show chunks of it and build up a network of ideas around each chunk. This also means that the text being worked on becomes part of the system, rather than remaining isolated, say, as a PDF or other representation. This also got me thinking about the Plazi project, where taxonomic papers are being broken into component chunks (e.g., figures, taxonomic descriptions, etc.) and these are then being stored in various places and reassembled - rather like Frankenstein's monster - in new ways, for example in GBIF (e.g., https://www.gbif.org/species/166240579) or Species-ID (see doi:10.3897/zookeys.90.1369 ). One thing I've always found a little jarring about this approach is that you lose the context of the work that each component was taken from. Yes, you can find a link to the original work and go there, but what if you could seamlessly click on the paragraph or figure see them as part of the original article? Imagine we had all the taxonomic literature available in this way, so that we can cite any chunk, remix it (which is a key part of floras and other taxonomic monographs), but still retain the original context?

Summary

To come back full circle, in some ways tools like Obsidian and Roam are old hat, we've had wikis for a while, the idea of loading texts into wikis is old (e.g., Wikisource), backlinks are nothing new, etc. But there's something about seeing clean, elegant interpretations of these ideas, free of syntax junk, and accompanied by clear visions of how software can help us think. I'm not sure I will use either app, but they have given me a lot of food for thought.