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Slides from a presentation to Biodiversity Informatics course, Stockholm, 16-09-2009
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Biodiversity Informatics
Ideas
• 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
Unknown knowns
Things we know …without knowing that we know
Melissotarsus insularis
Melissotarsus insularis no hit
CASENT0107663-D01 DQ176312
Melissotarsus sp. BLF m1DQ176312
CASENT0107663-D01Melissotarsus insularis
1
Melissotarsus insularisMelissotarsus 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…
43
discovering new species…
44
publishing papers…
45
Some of this knowledge is being broadcast using RSS
46
We want RSS feeds that
• Have timestamps
• Are georeferenced
• Have taxonomic names as tags
47
Geo RSS
geotagged (latitude, longitude, woeid)
taxonomic name (machine tags)
timestamp
like
48
But what if no RSS?
49
We can make it ourselves
http://bioguid.info/rss
Secret sauce(= screen scraping)
Web page RSS
50
Then add tags using services
Georeferencing
Taxonomic names
51
Now we have RSS…
52
53
…is anybody listening?54
Challenge: aggregate and display RSS
Merge RSS feeds, add missing georeferencing and taxonomic names
Display where, when, what
55
http://bioguid.info/ebio09/www/3d
Visualising biodiversity digitisation in real time56
Identifiers
Digital Object Identifier(DOI)
Identifies a publication
Globally unique
10.1016/j.ympev.2006.04.006
Paper
Why have DOIs?
Link rot
Refs
2006
Cites
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
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
Versions1 2 3 4
History flow
Afrotheria
EOL
Semantic wikis
(or, what’s wrong with Wikipedia?)