University of Glasgow

Roderic Page

While working with linked data and ways to explore and visualise
information, I keep coming back to the [Haystack
project](https://en.wikipedia.org/wiki/Haystack_(MIT_project)), which is
now over a decade old. Among the tools developed was the Haystack
application, which enabled a user to explore all sorts of structured
data. Below is a screen shot of Haystack showing a sequence for [Homo
sapiens cyclin T1 (CCNT1), transcript variant a,
mRNA](https://www.ncbi.nlm.nih.gov/nuccore/NM_001240.4/). Note the use
of a LSID to identify the sequence (LSIDs were actively being used to
identify bioinformatics resources)
**urn:lid:ncbi.nlm.nih.gov.lsid.i3c.org:genbank:nm_001240**.  
  

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For some background on the Haystack project see **How to Make a Semantic
Web Browser**
[DOI:10.1145/988672.988707](https://doi.org/10.1145/988672.988707)
([PDF](http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.4.5356&rep=rep1&type=pdf))
and **Haystack: A Customizable General-Purpose Information Management
Tool for End Users of Semistructured Data**
[PDF](http://www-db.cs.wisc.edu/cidr/cidr2005/papers/P02.pdf).  
One reason I keep coming back to the Haystack project is the notion of
having a **personal** space for exploring linked data. One of the
challenges of having a large knowledge graph is that it becomes hard to
have \"local\" queries. That is, queries which are restricted to a
subset of things that you care about.  
  
For example, while playing around with Ozymandias I keep coming across
interesting species, such as *Milyeringa justitia* (see [FIGURE 5 in A
new species of the blind cave gudgeon Milyeringa (Pisces: Gobioidei,
Eleotridae) from Barrow Island, Western Australia, with a redescription
of M. veritas
Whitley](https://ozymandias-demo.herokuapp.com/?uri=https://doi.org/10.5281/zenodo.220763)).  
  

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If I want to explore this taxon in more detail I\'d like to have the
original description, any relevant DNA sequences (e.g.,
[MG543430](https://www.ncbi.nlm.nih.gov/nuccore/MG543430.1)), any papers
publishing those sequences (e.g., [Multiple molecular markers reinforce
the systematic framework of unique Australian cave fishes
(Milyeringa : Gobioidei)](https://doi.org/10.1071/ZO18008)), and
phylogenetic analyses such as the paper [The First Record of a
Trans-Oceanic Sister-Group Relationship between Obligate Vertebrate
Troglobites](https://doi.org/10.1371/journal.pone.0044083) which
establishes a link between *Milyeringa* and a genus of cave fish endemic
to Madagascar (*Typhleotris*).  
  
What I\'d like to be able to do is collect all these sources (ideally by
simply bookmarking the links), saving them as a \"collection\", then at
some point exploring what the knowledge graph can tell me. The
importance of having a collection is so that I can tell the knowledge
graph that I just want to explore a subset of information. Without a
collection it can be tricky to limit the scope of queries. For example,
given a global knowledge graph such as Wikidata, how would you query
just species found in Australia? You would typically rely on the species
having either a property (\"found in Australia\"), or perhaps an
identifier that is only used for Australian species. Neither of these is
particularly satisfactory, especially if there isn\'t a property that
fortuitously matches the scope or your inquiry.  
Hence, I\'m interested in having collections: lists of entities that I
want to know more about. I need ways to create these collections, ways
to describe them, and ways to explore them. In some ways the collections
feature of EOL was close to what I\'m after. In the previous version of
EOL you could \"collect\" taxa that you were interested in (for example,
species that were blue) (see [I think I now \"get\" the Encylopedia of
Life](https://iphylo.blogspot.com/2011/09/i-think-i-now-encylopedia-of-life.html)).
Sadly, collections (along with JSON-LD export and stable image URLs)
have vanished from the new EOL (which seems to be in a death spiral
driven by some really unfortunate decisions). And collections need to be
able to contain any entity, not just taxa.  
  
One way to represent collections in the linked data world is using RSS
feeds, or their schema.org descendant, the
[DataFeed](https://schema.org/DataFeed) (see also Google\'s [Data Feed
Validation Tool](https://actions.google.com/tools/feed-validator/u/0/)).
So, we could collect a series of things we are interested in, create the
corresponding DataFeed, import that into our Knowledge Graph and that
would give us a way to scope our queries (using membership of the
DataFeed to select the species, papers, sequences, etc. that we are
interested in). As an aside, there\'s also some overlap with another MIT
project of old, David Huynh\'s
[Parallax](http://people.csail.mit.edu/dfhuynh/projects/parallax/)
project which explored querying on a set of objects, rather than one
object at a time. This is the functionality that a collection gives you
(if you have a query language like SPARQL which can work on sets of
things).  
  
Returning to Haystack, I\'m intrigued by the idea of building a personal
linked data browser. In other worlds, a browser that stores data that is
relevant to projects you are working on (e.g., blind fish) as
collections (data feeds), but can query a global knowledge graph to
augment that information. SPARQL supports federated queries, so this is
eminently doable. The local browser would have its own triple store,
which could be implemented using [Linked Data
Fragments](http://linkeddatafragments.org/).  
  
For now this is just a jumble of poorly articulated ideas, but I think
much of the power of linking data together will be lost until we have
simple tools that enable us to explore the data in ways that are
relevant to what we actually want to know. Haystack gives us one model
of what such a tool could look like.


While working with linked data and ways to explore and visualise information, I keep coming back to the Haystack project, which is now over a decade old. Among the tools developed was the Haystack application, which enabled a user to explore all sorts of structured data. Below is a screen shot of Haystack showing a sequence for Homo sapiens cyclin T1 (CCNT1), transcript variant a, mRNA.

Rogue Scholar Beiträge

Notes on collections, knowledge graphs, and Semantic Web browsers