Stratigraphic concepts and agetagging

Stratigraphic 'homonyms' are quite common, a result of ambiguous placenames which have been used to name stratigraphic units. The stratigraphic terms used in Jens' post on Table Mountain stratigraphy nicely illustrate this:
He wrote about the South African 'Peninsula Formation' which is a synonym for the 'Peninsula Sandstone'. Unfortunately, this 'Peninsula Formation' is homonym to the 'Peninsula Formation' from British Columbia. The latter is of Cretaceous age, whereas the South African was formed during the Ordovician!

Geoscientists using stratigraphic terms surely have a clear concept of what they mean. However, whereas for human readers it may be easy to determine such a concept by lithological descriptions or the broader geological or tectonic context, this is much harder for computer algorithms and thus, agetagging.
Fortunately, the regional context can easily be discovered by geotagging technologies, therefore the geographic concept of a stratigraphic term is most important. Stratigraphic homonyms may exist at much lower regional level, e.g. from different provinces or states and most likely there are also significant conceptual differences between scientists. etc etc. However, such regional concepts are sufficient for the approximation for our agetagging purposes. The concept of a South African 'Peninsula Formation' is surely completey different from the Canadian.

.. a lot of complications with 'strato-semantic' text analyis.. stratigraphic analysis of geoscientific texts requires a combined approach, good agetagging is not possible without geotagging.

Stratigraphy for web searches: Agesearch

This is a screenshot of Snet's latest toy: Agesearch. It is a demonstration mashup of basically two web services, the Google API as well as our own Ageparser REST service. I will post more technological details about all this soon.

Agenames is a scientific web search engine which allows to estimate the "stratigraphy" of web search results. It scans found web pages for names of stratigraphic units, e.g. litho-, chrono or biostratigraphic zones, and displays the best matching stratigraphic context of the search term.

It can be useful if you need a quick estimate on the stratigraphic context of e.g. a geographic region or a distinct fossil name try e.g. this search for Morozovella angulata. You can also do some fun queries, e.g. to give an overview on the stratigraphic expertise of one of your colleagues if you enter his name.

Chronotagging vs. agetagging

The new version of ageparser is almost ready to be released, so I was thinking which term would be appropriate to describe what ageparser does.

Ageparser V.2 is going to provide a REST webservice which will analyse strings or webpages for stratigraphically relevant terms and return the weighted results (the identified stratigraphical units and their chronostratigraphic position) as JSON or XML. So basically, the service returns a list of stratigraphic terms which can be use to describe or tag the content of a document. Therefore I thought something like 'agetagging' or 'chronotagging' perfectly describes what ageparser does.

After googling for those terms I found that 'chronotagging' is already used when a page is tagged with a specific date. But 'agetagging' seems to be a term which does not yet have another meaning, so I probably will use 'agetagging'..

Citation parsing

The next version of ageparser will extensively use regular expressions to identify stratigraphic terms. While working on this, I also played with some regular expressions which are useful to identify citations within a scientific document and to parse authors and year of these citations. I assume this is a quite common task for some of you, so maybe you find some of the following expressions useful for your own code:


Pattern for common person names:

$personpat=(([Bb][Ee][Nn]\s|[Dd][Ee]\s[Ll][Aa]\s|P'|[Dd]'|[vV][Aa][Nn]\s|[vV][Oo][Nn]\s|[dD][eE][lL]?\s|[dD][iI]\s)?[ÄÖÜA-Z]{1}[A-ZÄÖÜÒÓÀÉÈóòäöüàéèâa-z-]{1,})

Pattern for authors:

$citpersonpat=$personpat."{1}(,\s".$personpat.",?)?((\sand\s".$personpat.")|((,\s".$personpat.",?)?\set al(\.|[i]{2})))?"

And two patterns for citations:

$citpattern1="[\s\.]{1}(".$citpersonpat.")\s\([0-9]{4}[a-z]?\)"
$citpattern2="[\s\.]{1}[\(,;]?(".$citpersonpat.")[,;]?\s[0-9]{4}[a-z]?[\),;\.\s]"

Agenames Vienna presentation

The slides of the talk (Google docs version) Jens gave on Agenames during the EGU 2008 are available here:

http://docs.google.com/Presentation?id=dfx3hqfg_7gftng9dm

A preview of the new Stratigraphy.net look

For quite a while we have been very unhappy with the old Snet homepage. The content is completely outdated and simply does no more reflect or promote our current activities. Further, after more than 5 years we found it was really time to reconsider the overall look of the homepage ;)
The old version was based on the CMS Contenido which is nice, but develloping modules for such a system e.g. a search interface allowing direct access to Snet data is a pain. Further, contenido now is popular enough to attract hackers which forces us webmasters to carefully watch the latest vulnerability reports, thus frequently perform security fix updates.

Therefore I decided to completely redesign the Snet homepage. The new version will be home brewn, slimmer but more informative. It will concentrate more on content, Snet data , services and news.

To keep maintenance costs as low as possible, Snet 2 will support major standard protocols to ingest content from various sources. For example we will use OAI-PMH to collect data from Agenames, Taxonconcept (and possibly other 3d party sources). It will also use RSS feeds to include news from all Snet projects as well as from this blog.

More datails on the new Snet architecture will be published here soon. By now I would like to invite those interesed to visit the first beta of Snet2 here:
http://www.stratigraphy.net/Snet2.

Introducing Agenames

We are proud to announce a first 'alpha' release of 'Agenames' , a new Stratigraphy.Net project we started last year.

Agenames is very much inspired by the geonames initiative which collects and publishes geographical names and their coordinates. In analogy, Agenames aims to collect stratigraphic terms in relation to their chronostratigraphic position (relative age).
So if you need to find out what e.g. the 'Ammergauer Schichten' or the 'Black Donald Pluton' means Agenames might help..

But Agenames will offer more! We have started some first experiments with Ageparser a text parsing tool which uses the Agenames index and is able to scan documents for stratigraphic terms, thus identify the stratigraphic context of a publication.
We will use Ageparser for stratigraphic indexing of geoscientific documents with the ultimate goal of a 4D (space and time) search engine ... sometimes...

To learn more visit the Agenames homepage at http://agenames.stratigraphy.net or visit the EGU 2008 in Vienna where Jens will give a talk on Agenames at Wednesday, 16 April 2008.