Summary slides for AntCat workshop August 24-26 San Francisco, CA

1. Global Names Recognition and
Discovery (GNRD)
• High throughput, queue-based « skin » on
multiple processes of scientific name-finding
engines
– NetiNeti: Python, machine-learning-based
– TaxonFinder: Perl, dictionary-based
• Inputs: any file, URL, free-form text
– Uses Docsplit gem (Tesseract OCR as needed)
– Can send gzip request
• Outputs: JSON/xml
– Scientific names & their character offsets
– OCR text
– Resolved names

3. GNRD Clients & Applications

4. 15,000 OCR’d articles, 1868 - 2002
All with DOIs
158,000 unique scientific names
92,000 vernaculars
20,000 entities

6. No Consistency in Search APIs
{
"totalResults": 152,
"startIndex": 1,
"itemsPerPage": 30,
"results": [
{
"id": 14349,
"title": "Ursus",
"link":
"http://eol.org/14349?action=overview&controller=taxa",
"content": "Ursus Linnaeus, 1758; Ursus; Ursus
(genus); Ursus (genus) Linnaeus, 1758; Ursus Arctos
Bruinosus"
},
{ ... },
],
"first": "http://eol.org/api/search/Ursus.json?page=1",
"self": "http://eol.org/api/search/Ursus.json?page=1",
"next": "http://eol.org/api/search/Ursus.json?page=2",
"last": "http://eol.org/api/search/Ursus.json?page=6"
}
http://eol.org/api/search/1.0.json?q=Ursus http://api.gbif.org/name_usage/search?q=Ursus
{
offset: 0,
limit: 20,
endOfRecords: false,
count: 77,
results: [
{
datasetTitle: "English Wikipedia Species Pages",
parent: "Ursidae",
kingdom: "Animalia",
phylum: "Chordata",
clazz: "Mammalia",
order: "Carnivora",
family: "Ursidae",
genus: "Ursus »,
scientificName: "Ursus",
canonicalName: "Ursus",
authorship: "",
nameType: "WELLFORMED",
rank: "GENUS",
…

7. Use Darwin Core Terms

8. OpenURL
• Created in late 1990s by a Flemish librarian
• eg v0.1
http://resolver.example.edu/cgi?genre=book
&isbn=0836218310&title=The+Far+Side+Galle
ry+3
• But no specification for response structure!!!

9. bibJSON
{
"title": "Open Bibliography for Science, Technology and Medicine",
"author":[
{"name": "Richard Jones"},
{"name": "Mark MacGillivray"},
{"name": "Peter Murray-Rust"},
{"name": "Jim Pitman"},
{"name": "Peter Sefton"},
{"name": "Ben O'Steen"},
{"name": "William Waites"}
],
"type": "article",
"year": "2011",
"journal": {"name": "Journal of Cheminformatics"},
"link": [{"url":"http://www.jcheminf.com/content/3/1/47"}],
"identifier": [{"type":"doi","id":"10.1186/1758-2946-3-47"}]
}

10. Recommendation
• Use DwC terms as query params for find or ‘q’ for
search
• Use DwC terms as keys in JSON responses
http://www.antweb.org/description.do?name=claripes%2
0orbiculatopunctatus&genus=camponotus&rank=species&
project=worldants
http://www.antweb.org/description.do?specificEpithet=cla
ripes&infraspecificEpithet=orbiculatopunctatus&genus=ca
mponotus&taxonRank=species&project=worldants

11. Canadensys:
Vascular Plants of Canada
(VASCAN)
Luc Brouillet, Peter Desmet, et al.

12. http://data.canadensys.net/vascan

15. http://data.canadensys.net/vascan/name/Carex%20abbreviata

16. http://data.canadensys.net/vascan/taxon/26512

18. http://doi.org/10.3897/phytokeys.25.3100

20. http://creativecommons.org/publicdomain/zero/1.0/

21. Suggestions for AntCat
• Run literature through GNRD
• Simplify web presence with concentration on
search as the entry point
– index all available content
– Present « pages » as declaration of relationships
• Use Darwin Core terms in « find » and
« search » services
• Make DwC-A, CC-0 waiver, data paper &
publish to GBIF, make accessible to GN