University of Glasgow

Roderic Page

Following on from the previous post [Rethinking annotating biodiversity
data](http://iphylo.blogspot.com/2014/03/rethinking-annotating-biodiversity-data.html),
here are some more thoughts on annotating biodiversity data.  
  

### Annotations as sticky notes

  
I get the sense that most people think of annotations as \"sticky
notes\" that someone puts on data. In other words, the data is owned by
somebody, and anyone who isn\'t the owner gets to make comments, which
the owner is free to use or ignore as they see fit. With this model, the
focus is on how the owner deals with the annotations, and how they
manage the fact that their data may have changed since the annotations
were made.  
  
This model has limitations. For a start, it privileges the \"owner\",
and puts annotators at their mercy. For example, I posted an issue
regarding a record in the Museum of Comparative Zoology Herpetology
database (see
<https://github.com/mcz-vertnet/mcz-subset-for-vertnet/issues/1>).
VertNet has [adopted GitHub to manage annotations of collection
data](http://iphylo.blogspot.com/2014/01/vertnet-starts-issue-tracking-using.html),
which is nice, but it only works if there\'s someone at the other end
ready to engage with people like me who are making annotations. I
suspect this is mostly not going to be the case, so why would I bother
annotating the data? Yes, I know that VertNet has only just set this up,
but that\'s missing the point. Supporting this model requires customer
support, and who has the resources for that? If I don\'t get the sense
that someone is going to deal with my annotation, why bother?  
  
So, the issues here are that the owner gets all the rights, the
annotators have none, and in practice the owners might not be in a
position to make use of the annotations anyway.  
  

### Wikis

  
OK, if the owner/annotator model doesn\'t seem attractive, what about
wikis? Let\'s put the data on a wiki and let folks edit it, that\'ll
work, right? There\'s a lot to be said in favour of wikis, but there\'s
a disadvantage to the basic wiki model. On a wiki, there is one page for
an item, and everyone gets to edit that same page. The hope is that a
consensus will emerge, but if it doesn\'t then you get edit wars (e.g.,
[When taxonomists wage war in
Wikipedia](http://iphylo.blogspot.com/2009/09/when-taxonomists-wage-war-in-wikipedia.html)).
If you\'ve made an edit, or put your data on a wiki, anyone can
overwrite it. Sure, you can roll back to an earlier version, but so can
anyone else.  
  
Wikis bring tools for community editing, but overturn ownership
completely, so the data owner, or indeed any individual annotator has no
control over what happens to their contributions. Why would an expert
contribute if someone else can undo all their hard work?  
  

### Social data

  
So, if sticky notes and wikis aren\'t the solution, what is? I\'ve been
looking at [Fluidinfo](http://fluidinfo.com) lately. There\'s an
[interview
here](http://blogs.fluidinfo.com/fluidinfo/2012/04/24/interview-with-robert-scoble/),
and a [book here](http://shop.oreilly.com/product/0636920020738.do). The
company has gone quiet lately (apparently [focussing on enterprise
customers](http://www.quora.com/Fluidinfo/Is-Fluidinfo-still-alive)),
but what matters here is the underlying idea, namely \"social data\".  
  
Fluidinfo\'s model is that it is a database of objects (representing
things or concepts), and anyone can add data to those objects (they are
\"openly writable\"). The key is that every tag is linked to the user,
and by default you can only add, edit, or delete your own tags. This
means that if a data provider adds, say a bibliographic reference to the
database, I can edit it by adding tags, but I can\'t edit the data
provider\'s tags. To make this a bit more concrete, suppose we have a
record for the article with the DOI 10.1163/187631293X00262. We can
represent the metadata from CrossRef like this:  

::: {style="font-family:Courier"}
  
{  
\"\_id\": \"10.1163/187631293X00262\",  
\"crossref/doi\" : \"10.1163/187631293X00262\",  
\"crossref/title\" : \"A taxonomic review of the pondskater\...\",  
\"crossref/journal\" : \"Insect Systematics & Evolution\",  
\"crossref/issn\" : \[ \"1399-560X\", \"1876-312X\"\]  
}  
:::

  
Note the use of the namespace \"crossref\" in the tags. This is data
that, notionally, CrossRef \"owns\" and can edit, and nobody else. Now,
as I\'ve discussed earlier ([Orwellian metadata: making journals
disappear](http://iphylo.blogspot.com/2011/09/orwellian-metadata-making-journals.html))
some publishers have an annoying habit of retrospectively renaming
journals. This article was published in *Entomologica Scandinavica*,
which has since been renamed *Insect Systematics & Evolution*, and
CrossRef gives the latter as the journal name for this article. But most
citations to the article will use the old journal name. Under the social
data model, I can add this information (in **bold**):  

::: {style="font-family:Courier"}
  
{  
\"\_id\": \"10.1163/187631293X00262\",  
\"crossref/doi\" : \"10.1163/187631293X00262\",  
\"crossref/title\" : \"A taxonomic review of the pondskater\...\",  
\"crossref/journal\" : \"Insect Systematics & Evolution\",  
\"crossref/issn\" : \[\"1399-560X\", \"1876-312X\"\],  
**\"rdmpage/journal\" : \"Entomologica Scandinavica\",\"rdmpage/issn\" :
\[\"0013-8711\" \]**  
}  
:::

  
My tags have the namespace \"rdmpage\", so they are \"mine\". I haven\'t
overwritten the \"crossref\" tags. Somebody else could add their own
tags, and of course, CrossRef could update their tags if they wish. We
can all edit this object, we don\'t need permission to do so, and we can
rest assured that our own edits won\'t be overwritten by somebody
else.  
  
This model can be quite liberating. If you are a data provider/owner,
you don\'t have to worry about people trampling over your data, because
you (and any users of your data) can simply ignore tags not in your
namespace (\"ignore those rdmpage\' tags, that Rod Page chap is clearly
a nutter\"). Annotators are freed from their reliance on data providers
doing anything with the annotations they created. I don\'t care whether
CrossRef decides to revert the journal name *Insect Systematics &
Evolution* to *Entomologica Scandinavica* for earlier article (or not),
I can just use the \"rdmpage/journal\" (if it exists) to get what I
think is the appropriate journal name. My annotations are immediately
usable. Because everyone gets to edit in their own namespace, we don\'t
need to form a consensus, so we don\'t need the version control feature
of wikis to enable roll backs, there are no more edit wars (almost).  
  

### Implementation

  
A key feature of the Fluidinfo social data model is that the data is
stored in a single, globally accessible place. Hence we need a global
annotation store. Fluidinfo itself doesn\'t seem to have a publicly
accessible database, I guess in part because managing one is a major
undertaking (think [Freebase](http://freebase.org)). Despite Nicholas
Tollervey\'s post ([FluidDB is not CouchDB (and FluidDB\'s secret
sauce)](http://ntoll.org/article/fluiddb-is-not-couchdb)), I think
CouchDB is exactly the way I\'d want to implement this (it\'s here, it
works, and it scales). The \"secret sauce\" is essentially application
logic (every key has a namespace corresponding to a given user).  
  
The more I think about this model the more I like it. It could greatly
simplify the task of annotating biodiversity data, and avoid what I fear
are going to be the twin dead ends of sticky note annotation and wikis.


Following on from the previous post Rethinking annotating biodiversity data, here are some more thoughts on annotating biodiversity data.
<strong>
 Annotations as sticky notes
</strong>
I get the sense that most people think of annotations as "sticky notes" that someone puts on data. In other words, the data is owned by somebody, and anyone who isn't the owner gets to make comments, which the owner is free to use or ignore as they see fit.

Messages de Rogue Scholar

More on annotating biodiversity data: beyond sticky notes and wikis