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Biodiversity Informatics

Biodiversity Informatics Course Presentation

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Slides from a presentation to Biodiversity Informatics course, Stockholm, 16-09-2009

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Page 1: Biodiversity Informatics Course Presentation

Biodiversity Informatics

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Ideas

• Linking• Mashups• Data mining• RSS• Identifiers• Errors• Wikis

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Linking

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Apomys datae

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Apomys specimen

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How do we integrate these data?

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Why integrate?

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Learn stuff we don’t know

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• 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

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Unknown knowns

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Things we know …without knowing that we know

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Melissotarsus insularis

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Melissotarsus insularis no hit

CASENT0107663-D01 DQ176312

Melissotarsus sp. BLF m1DQ176312

CASENT0107663-D01Melissotarsus insularis

1

Melissotarsus insularisMelissotarsus sp. BLF m1 =

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No one source has all the answers

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Joining the dots

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Mashups

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Single source

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Many sources

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Combine sources

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ispecies.org

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Merge things your way

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Don’t like iSpecies?

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Make your own!

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Data mining

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Text mining

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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

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RSS

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Visualising biodiversity digitisation in real time

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gathering new data…

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discovering new species…

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publishing papers…

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Some of this knowledge is being broadcast using RSS

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We want RSS feeds that

• Have timestamps

• Are georeferenced

• Have taxonomic names as tags

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Geo RSS

geotagged (latitude, longitude, woeid)

taxonomic name (machine tags)

timestamp

like

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But what if no RSS?

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We can make it ourselves

http://bioguid.info/rss

Secret sauce(= screen scraping)

Web page RSS

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Then add tags using services

Georeferencing

Taxonomic names

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Now we have RSS…

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…is anybody listening?54

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Challenge: aggregate and display RSS

Merge RSS feeds, add missing georeferencing and taxonomic names

Display where, when, what

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http://bioguid.info/ebio09/www/3d

Visualising biodiversity digitisation in real time56

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Identifiers

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Digital Object Identifier(DOI)

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Identifies a publication

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Globally unique

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10.1016/j.ympev.2006.04.006

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Paper

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Why have DOIs?

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Link rot

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Refs

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2006

Cites

2006

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Forward Cites

2006 2009

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Shoulders of giants

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progress is incremental

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reuse past results

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Forward Cites

2006 2008

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Species

Genes

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data linking

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data citation

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Need tools to:

• Resolve identifiers

• Create new identifiers

• Find existing identifiers

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http://bioguid.info/openurl/

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Errors

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

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demo

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The Carmen Electra argument for Open Access

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reuse data

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Electra pilosa

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Carmen Electra versus Electra

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reuse data

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Homo sapiens

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AJ711044

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should be AJ971044

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how do I fix this error?

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Closed

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Can’t easily fix

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Open…

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…and editable

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Anybody could fix it

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Wikis

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Wikis

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Versions1 2 3 4

History flow

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Afrotheria

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EOL

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Semantic wikis

(or, what’s wrong with Wikipedia?)