Biodiversity Informatics

Ideas Linking Mashups Data mining RSS Identifiers Errors Wikis

Linking

Mashups

Data mining

RSS

Identifiers

Errors

Wikis

Linking

Apomys datae

Apomys specimen

How do we integrate these data?

Why integrate?

Learn stuff we don’t know

There are known knowns , things we know that we know There are known unknowns , things we now know we don’t know But there are also unknown unknowns , things we do not know we don't know

There are known knowns , things we know that we know

There are known unknowns , things we now know we don’t know

But there are also unknown unknowns , things we do not know we don't know

Unknown knowns

Things we know …without knowing that we know

Melissotarsus insularis

Melissotarsus insularis no hit CASENT0107663-D01 DQ176312 Melissotarsus sp. BLF m1 DQ176312 CASENT0107663-D01 Melissotarsus insularis 1 Melissotarsus insularis Melissotarsus sp. BLF m1 =

No one source has all the answers

Joining the dots

Mashups

Single source

Many sources

Combine sources

ispecies.org

Merge things your way

Don’t like iSpecies?

Make your own!

Data mining

Text mining

Morphological and molecular description of Haematoloechus meridionalis n. sp. (Digenea: Plagiorchioidea: Haematoloechidae) from Rana vaillanti brocchi of Guanacaste, Costa Rica Halipegus eschi n. sp. (Digenea: Hemiuridae) in Rana vaillanti from Guanacaste Province, Costa Rica Haematoloechus danbrooksi n. sp. (Digenea: Plagiorchioidea) from Rana vaillanti from Los Tuxtlas, Veracruz, Mexico

RSS

Visualising biodiversity digitisation in real time

gathering new data…

discovering new species…

publishing papers…

Some of this knowledge is being broadcast using RSS

We want RSS feeds that Have timestamps Are georeferenced Have taxonomic names as tags

Have timestamps

Are georeferenced

Have taxonomic names as tags

like Geo RSS geotagged (latitude, longitude, woeid) taxonomic name (machine tags) timestamp

But what if no RSS?

We can make it ourselves http://bioguid.info/rss Secret sauce (= screen scraping) Web page RSS

Then add tags using services Georeferencing Taxonomic names

Now we have RSS…

… is anybody listening?

Challenge: aggregate and display RSS Merge RSS feeds, add missing georeferencing and taxonomic names Display where, when, what

http://bioguid.info/ebio09/www/3d Visualising biodiversity digitisation in real time

Identifiers

Digital Object Identifier (DOI)

Identifies a publication

Globally unique

10.1016/j.ympev.2006.04.006

Paper

Why have DOIs?

Link rot

Refs

Cites 2006 2006

Forward Cites 2006 2009

Shoulders of giants

progress is incremental

reuse past results

Forward Cites 2006 2008

Species Genes

data linking

data citation

Need tools to: Resolve identifiers Create new identifiers Find existing identifiers

Resolve identifiers

Create new identifiers

Find existing identifiers

http://bioguid.info/openurl/

Errors

http://iphylo.org/~rpage/challenge

demo

The Carmen Electra argument for Open Access

reuse data

Electra pilosa

Carmen Electra versus Electra

reuse data

Homo sapiens

AJ711044

should be AJ971044

how do I fix this error?

Closed

Can’t easily fix

Open…

… and editable

Anybody could fix it

Wikis

Wikis

Versions 1 2 3 4 History flow

Afrotheria

EOL

Semantic wikis (or, what’s wrong with Wikipedia?)