Tuesday 8 May 2007

Tapir, LSIDs and TDWG and what it all means...

More on the categorising of flora and fauna. Following on from my post of 1st May, here, a discussion with Paul and Lynda has clarified a bit more about what all the acronyms mean and what the plans for the future are.

LSIDs are a categorising system that sets out to bring digital collections management in biodiversity up to a web 2.0 standard. Ideally it replaces and encompasses the two previous standards for flora and fauna, makes the data accessible and searchable, and allows much greater aggregation of data.
In a practical sense, what this means is that you can search for and find an object (which can be an actual specimen, but not only a specimen!), and then, using its LSID, locate other objects related to it by location, by species, by characteristics, by institution, or by any information that is conveyed by the LSID.

To borrow from the LSID website:

Every LSID consists of up to five parts: the Network Identifier (NID); the root DNS name of the issuing authority; the namespace chosen by the issuing authority; the object id unique in that namespace; and finally an optional revision id for storing versioning information. Each part is separated by a colon to make LSIDs easy to parse.


So what does this do for the biodiversity community? Well, if museums et al take up the system, it means that all this data is available online: for research purposes, for species monitoring, for mapping and locating endangered and rare species, and so enabling a greater and more immediate response to management and planning for the future. Again, the Hennes article comes to mind, with its discussion about the future possibilities for museums and their collections.



How is it implemented?
Unlike other online cataloguing systems, this would be applied at the level of the institution. If the institution already has a DOI system in place, it may need tweaking to comply with LSID standards. The internal museum system would not have to be changed, however, as the LSID is divided into component parts (described above).
It is overseen by TAPIR (TDWG Access Protocol for Information Retrieval)
As the website says:



TAPIR combines and extends features of the BioCASe and DiGIR protocols to create a new and more generic means of communication between client applications and data providers using the Internet.


So, TAPIR oversees the implementation of the protocol. If you feel brave enough to tackle a sea of acronyms you can check out the TAPIR wiki.

Please let me know if any of this is inaccurate, i have done my best to put it in layperson terms. Conceptually it sounds like a great idea to me. We also discussed The machine is eating us, as an example of a great way to convey what are conceptually complicated ideas in a simple, effective, interesting format. Are there other, successful ways to deal with these issues in a very short timeframe? that is the upcoming challenge.

18 comments:

Lynda Kelly said...

Several weeks ago Jesse Ausubel, Chair of the Board of the "http://www.eol.org/">Encyclopedia of Life gave a talk at the Museum. They have recently launched their website and the FAQ page gives a good overview of this ambitious project.

Basically the premise is to have "a web site for every species" which contains, not only general information about a species, but an underlying archivce of all scientific papers and other related material as part of the species record.

As Jesse said in his presentation:
“Imagine an electronic page for each species of organism on Earth, available everywhere by single access on command. The page contains the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits. The page opens out directly or by linking to other databases ... It comprises a summary of everything known about the species’ genome, proteome, geographical distribution, phylogenetic position, habitat, ecological relationships and, not least, its perceived practical importance for humanity."

This sounds like something to keep on top of, and I'm wondering if the LSID/TDWG group will be involved somehow??

Lynda Kelly said...

Mel: Lee Belbin, Manager of the TDWG Infrastructure Project mentioned that they would like two stories/videos about the LSID/TDWG projects. The examples he gave us that they like are The Machine is Us/ing Us and The Encyclopedia of Life - the EOL I haven't seen before and it's totally cool (but looks expensive...).

At this stage I think we should run a thread on the TDWG blog and invite both generalists and specialists into our conversation. What do others think?

TasiLee said...

TDWG is indeed involved with the EoL project. In fact TAPIR + LSIDs are two key components of GBIF's Universal Biodiversity Data Bus (UBDB or as Paddy from EoL calls it - the Oobe Doobie). EoL has stated that it would use TDWG standards when it came to moving 'biodiversity' data around - which is a BIG part of what EoL will do. LSIDs will become the the core identifiers of biological (or any other type) of object, and TAPIR provides the mechanism to query and aggregate responses across the network.

mel said...

I don't think it really matters where it is, especially if we are interested in testing the use of blogging in the first place, and how it works (or doesn't) for the museum. having said that, i am happy to converse anywhere, as long as there is someone who can explain the acronysms to me!
We are certainly off to a good start already.

TasiLee said...

The TDWG Blog is being setup in the next hour or so to accept posts from any user registered on the TDWG site (see http://www.tdwg.org/membership/registration/).

The blog has an RSS feed at http://www.tdwg.org/blog/rss.xml.

Also of interest: The EoL project just hit Newsweek (http://www.msnbc.msn.com/id/18580428/site/newsweek/) with a prominant mention of the 'inspirational video'.

Things are really hotting up in the biodiversity arena! A good thing.

Lynda Kelly said...

Thanks Lee - I've signed up and am looking forward to working in the wonderful world of acronyms!

Renato De Giovanni said...

Mel, regarding TAPIR and the idea of making a video, you probably don't need to worry about most acronyms and strange names that you find in the Wiki. Sometimes they are related to historical things, like the previous protocols DiGIR and BioCASe; sometimes they are related to the software implementations, like PyWrapper and TapirLink; sometimes they are related to other data standards that can be exchanged through TAPIR, like ABCD, DarwinCore, TCS; sometimes they are related to similar technologies, like WFS.

In my opinion none of these things are worth mentioning in a video for a non-technical audience. The most important thing is to grasp the main idea of TAPIR, understand how it works and what it can do. A good starting point is the executive summary that we just prepared (it's only a first version, so we're welcoming any suggestions).

By the way, I somehow always associate TAPIR with the idea of "unleashing data". It also comes to my mind a picture of someone opening a drawer full of specimens. TAPIR allows many database drawers to open at the same time to deliver you the data you want...

mel said...

Renato
that's a very good executive summary - it makes TAPIR much clearer. I also like the analogy of the drawers, filled with specimens, being opened - a nice visual metaphor.
In technical terms, is it anything like using php and My SQL to mine a database?
I am glad you defined the audience, it makes the project simpler. Lynda mentioned two stories - is one about LSIDs and one about TAPIR?

Renato De Giovanni said...

Yes, I think Lee mentioned two videos: one for TAPIR and another for LSIDs.

About your comparison with PHP and MySQL, I'm not sure what kind of similarities you're trying to find.

- PHP and a MySQL database: There's only one database with a specific data structure. You write a PHP script that conects to the database and then you send one or more SQL queries to get the data you want.

- TAPIR network: There are several addresses on the Web (TAPIR accesspoints) that can be used to communicate with TAPIR data providers. You can use some kind of yellow pages service to discover these addresses. Once you have them, you can write a script in your favourite language to interact with the services. It's good practice to make sure that all services use the same abstraction layer and have the necessary capabilities before sending search requests. If these conditions are met, your script can interact in parallel with all services. A search request to one specific service can look like:

http://example.net/col_x?op=search&
m=*&filter=genus equals "Thylacinus"

* = address to an output model indicating the format of the response.

In this example, genus would actually be something like http://rs.tdwg.org/dwc/dwcore/Genus which is an identifier of a concept from DarwinCore. For each TAPIR provider using DarwinCore, this concept will be "mapped" to a specific field in a database.

This way you can remotely interact with many data providers without worrying about their operating system, type of database and database structure.

Trying to explain in a different way, if you want to use PHP for the task, instead of connecting to a MySQL database and sendng SQL queries, you will need to connect to several internet addresses sending HTTP requests according to the TAPIR protocol and then parsing the XML responses.

Not sure if this helps your understanding or not...

mel said...

Thanks Renato, I had another look at the executive summary and I think the mist is clearing...I think it is good to have this exchange, especially considering the videos will be aimed at the scientific layperson, which is what I am! And like anyone, to understand the concepts I look for analogies to areas I already know.

I keep returning to your metaphor of the opening drawers, and perhaps the next step from here would be an example of what data/info TAPIR (and LSID) allows you to see, compared to previous methods of data access.

Anonymous said...

I have set up a blog on the TDWG site now - you can get there thru
:-
http://www.tdwg.org/blog/blog-article/article/digital-stories-for-tapir-and-lsid/

You will need to register to comment

Anonymous said...

I have posted at TDWG - please go there to contribute
http://www.tdwg.org/blog/blog-article/article/digital-stories-for-tapir-and-lsid/

mel said...

This discussion is continuing over at TDWIG blog, with a dialogue on digital story development to explain TAPIR and LSID underway. please check this out

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