The Sam Adams talk
-
Upload
roderic-page -
Category
Science
-
view
256 -
download
0
Transcript of The Sam Adams talk
The Sam Adams talk
The Sam Adams talk
@rdmpage
http://iphylo.blogspot.com
1
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
24
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