Maastricht University

Egon Willighagen

[Kasabi](https://www.wikidata.org/wiki/Q128214915) was an innovative RDF
publishing platform from around 2011.
[Shortlived](https://web.archive.org/web/20130907095112/http://blog.kasabi.com/about/),
and maybe just too early. I published two open datasets there. One was
ChEMBL-RDF (see these
[posts](https://chem-bla-ics.linkedchemistry.info/tag/chembl)). The
second was a small data sets called
[ChemPedia](https://chem-bla-ics.linkedchemistry.info/2011/07/06/chempedia-rdf-2-kasabi.html),
a open science effort to crowdsource chemical names. This is still very
much needed, and possibly Wikidata could fill that gap, but it would
first need to be able to handle all labels as statements itself.

Anyway, just before they shutdown because of, I understood, lack of
commercial interest, they [archived all
data](https://archive.org/details/kasabi), including the ChemPedia
datasets. I was happy to be reminded about that, because I am not sure I
had archived that data.

#### References


Kasabi was an innovative RDF publishing platform from around 2011. Shortlived, and maybe just too early. I published two open datasets there. One was ChEMBL-RDF (see these posts). The second was a small data sets called ChemPedia, a open science effort to crowdsource chemical names. This is still very much needed, and possibly Wikidata could fill that gap, but it would first need to be able to handle all labels as statements itself.

Kasabi archive at the Internet Archive

I reported earlier how to I [uploaded the ChemPedia (RIP) data onto
Kasabi](http://chem-bla-ics.blogspot.com/2011/07/chempedia-rdf-3-uploading-data-to.html).
But for ChEMBL-RDF I have used the
[pytassium](https://github.com/iand/pytassium) tool, not just because it
has a cool name :) I discovered yesterday, however, that I did not write
down in this lab notebook, what steps I needed to take to reproduce it.
And I just wanted to uploaded new triples to the [ChEMBL-RDF data set on
Kasabi](http://kasabi.com/dataset/chembl-rdf).

The new triples I wanted to upload, link the [new public CHEMBL
identifiers](http://chembl.blogspot.com/2011/08/chembl-11-released.html)
(like [CHEMBL25 for
aspirin](https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/CHEMBL25))
to the internal ChEMBL database identifier I used for ChEMBL 09 for the
URIs. So, I am adding a lot of triples like:

:::: {.language-turtle .highlighter-rouge}
::: {.highlight}
``` highlight
 
```
:::
::::

And the pytassium code I use to upload this to Kasabi looks like:

:::: {.language-python .highlighter-rouge}
::: {.highlight}
``` highlight
import pytassium
import time

dataset = pytassium.Dataset('chembl-rdf','XXX')

# Store the contents of a turtle file
dataset.store_file('chemblids.nt', media_type='text/plain')
```
:::
::::

So, that omission in my log book has been corrected now.

#### References


I reported earlier how to I uploaded the ChemPedia (RIP) data onto Kasabi. But for ChEMBL-RDF I have used the pytassium tool, not just because it has a cool name :) I discovered yesterday, however, that I did not write down in this lab notebook, what steps I needed to take to reproduce it. And I just wanted to uploaded new triples to the ChEMBL-RDF data set on Kasabi.

ChEMBL-RDF: Uploading data to Kasabi with pytassium

![](/assets/images/kasabi.png){style="float: right;" width="200"}
[Kasabi](http://beta.kasabi.com/) is a new, RDF hosting service by
[Talis](http://www.talis.com/). It's still in beta, and I have been
testing their beta service with the [RDF
version](http://chem-bla-ics.blogspot.com/2009/11/chempedia-rdf-1-sparql-end-point.html)
I created of [ChemPedia Substances](http://metamolecular.com/chempedia/)
(the now no longer existing cool web service from
[MetaMolecular](http://metamolecular.com/) to draw and name organic
molecules).

Kasabi makes the RDF data available via a few APIs, depending on the
APIs selected by the uploader. I picked all five of them, just to see
how things work. Of direct interest are the SPARQL end point, but also
the option to host the data as dereferencable resources. Cool! That was
just what was missing for me.

Now, using the API requires you to get an account. This will allow
Kasabi to control the traffic, and as such creates a business model
around providing services around Open Data. I think this approach will
work. But just to make clear, this does mean you need to get an account
first, if you like to play with this data. Once you got an account, you
get an API key, and you can append that to any URI with
`?apikey=XXXX`{.language-plaintext .highlighter-rouge} to authenticate
yourself. I think this does mean Kasabi will have to go to a https
connection, which is not yet the case. Moreover, you will need to
subscribe to the data set too. That, in fact, with \#altmetrics in mind,
sounds really interesting :)

The ChemPedia RDF data is available at:
<http://beta.kasabi.com/dataset/chempedia-rdf>

This web page will give the five APIs, of which the augmentation one is
really interesting, but I have not played with that yet to say much
about it. The idea of that API is to augment RDF you post with data from
the data set. Like in a [augmented
reality](http://en.wikipedia.org/wiki/Augmented_reality). That should be
cool for mashups.

Now, the APIs I do understand include this SPARQL end point (remember to
add your API key!):

<http://labs.kasabi.com/explorer/sparql/sparql-endpoint-chempedia-rdf>

And the Linked Data feature. In the [next
post](http://chem-bla-ics.blogspot.com/2011/07/chempedia-rdf-3-uploading-data-to.html),
I will explain how I tweaked the original data, how I uploaded it, and
how this resulted in the dereferencable resources, like:

<http://data.kasabi.com/dataset/chempedia-rdf/substances/2-2595-7562-8125.html>

Note the links for RDF/XML, RDF/JSON, and Turtle, directly accessible by
replacing the .html extension with .rdf, .json, and .ttl respectively.
An API key does not seem required for this, which makes perfect sense.

It took me some chatting with the people from Talis, who have been very
helpful, as the whole platform was a bit overwhelming. But, for the
first time ever, I actually got Linked Open Data online, in a Linked
Data manner.

#### References


Kasabi is a new, RDF hosting service by Talis. It’s still in beta, and I have been testing their beta service with the RDF version I created of ChemPedia Substances (the now no longer existing cool web service from MetaMolecular to draw and name organic molecules).  Kasabi makes the RDF data available via a few APIs, depending on the APIs selected by the uploader. I picked all five of them, just to see how things work.

Messaggi di Rogue Scholar

Kasabi archive at the Internet Archive

ChEMBL-RDF: Uploading data to Kasabi with pytassium

ChemPedia-RDF #2: Kasabi