The Sam Adams talk

The Sam Adams talk

@rdmpage

http://iphylo.blogspot.com

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Numbers of new animal names

1923WWIWWII

http://www.organismnames.com/metrics.htm?page=graphs2

ImplicationsTaxonomists are working at capacity

Maybe we are running out of species to discover(!)

Most taxonomic work is in the past (legacy)

http://www.nature.com/scitable/content/growth-in-nucleotide-sequences-submitted-to-genbank-450684

Two graphs

Two graphs

taxonomysequencing

Focus on sequences= focus on phylogeny

taxonomysequencing

OneZoom.org

Visualise all barcodes

http://iphylo.org/~rpage/bold-map

Page R. Visualising Geophylogenies in Web Maps Using GeoJSON. PLOS Currents Tree of Life. 2015 Jun 23 . Edition 1. doi: 10.1371/currents.tol.8f3c6526c49b136b98ec28e00b570a1e

Page R. Visualising Geophylogenies in Web Maps Using GeoJSON. PLOS Currents Tree of Life. 2015 Jun 23 . Edition 1. doi: 10.1371/currents.tol.8f3c6526c49b136b98ec28e00b570a1e.11

Setting taxonomic information free

taxonomysequencing

Digitise the literaturehttp://biodiversitylibrary.orghttp://biostor.org

BioNameshttp://bionames.org

5 million (animal) names

1.6 million with publications

454,000 publications with digital identifier

DOIs, BHL, BioStor, PDFs, Gallica, etc.

Rethinking publications

Ted NelsonHyperlinks and hypermediaTwo-way links and transclusion= Xanadu

Tim Berners-LeeHTTP, URL, HTMLOne-way links= world wide web

Web pageOther web page

Web linking, one way, document-level, target doesnt know that it is linked to (cited), link can break (404)

textWorkSource

text

Xanadu linking, two way, fragment-level, source knows it is linked to, source content is embedded, links dont break

Xanadu

Ted Nelsons Xanadu project, linking and microcredit19

Wait, WTF has this to do with floras?!

A New Account of the Genus Horsfieldia (Myristicaceae), Pt 2W J J O De WildeThe Gardens' bulletin, Singapore 38(1): 55-144 (1985)

http://biostor.org/reference/175018

Horsfieldia lancifolia

Flora Malesiana. Series I - Seed Plants, Volume 14. Myristicaceae

Description

DescriptionFloraArticle

van Balgooy 3973 van Balgooy 3973

van Balgooy 3973 = http://www.gbif.org/occurrence/1139234988= http://bioportal.naturalis.nl/nba/result?nba_request=http%253A%252F%252Fapi.biodiversitydata.nl%252Fv0%252F%252Fspecimen%252Fget-specimen%252F%253FunitID%253DL.1769594&noMap

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Description

Article

Specimen

{"key": 1139234988,"scientificName": "Horsfieldia lancifolia W.J.J.O. de Wilde","kingdom": "Plantae","phylum": "Tracheophyta","order": "Magnoliales","family": "Myristicaceae","genus": "Horsfieldia","species": "Horsfieldia lancifolia","genericName": "Horsfieldia","specificEpithet": "lancifolia","taxonRank": "SPECIES","decimalLongitude": 121.75,"decimalLatitude": -2.25,"continent": "ASIA","stateProvince": "Sulawesi","year": 1979,"month": 7,"day": 11,"occurrenceID": "http://data.biodiversitydata.nl/naturalis/specimen/L.1769594}Data (GBIF)

Data

http://www.gbif.org/occurrence/1139234988 25

Xanadu in the 21st century?

text

ArticleAnnotations

table

annotationannotation

@hypothes_is

Annotating a scientific paper

Aggregating annotations (iPhylo)http://iphylo.blogspot.co.uk/2016/06/aggregating-annotations-on-scientific_30.html

http://iphylo.blogspot.co.uk/2016/06/aggregating-annotations-on-scientific_30.html30

Towards a biodiversity knowledge graph Research Ideas and Outcomes 2: e8767 (07 Apr 2016)doi: 10.3897/rio.2.e8767

GBIF and the problem of data

Data and feedback flow

Somethings wrong!

GBIF and the zika virushttp://iphylo.blogspot.co.uk/2016/04/the-zika-virus-gbif-and-missing.html

http://iphylo.blogspot.co.uk/2016/04/the-zika-virus-gbif-and-missing.html34

What if we treat data like source code

Original dataEdited data

SummarySequencing versus taxonomy?

Visualisation as a tool

Rethinking the nature of publications

The Biodiversity Knowledge Graph

Data as source code