Discussion seminar for the ENTO681 course. Starting points were: Wilson, 2003 - http://dx.doi.org/10.1016/S0169-5347(02)00040-X Mallet & Willmot, 2003 - http://dx.doi.org/10.1016/S0169-5347(02)00061-7 Godfray, 2002 - http://dx.doi.org/10.1038/417017a Doctorow, 2001 - http://www.well.com/~doctorow/metacrap.htm Author: Ana Dal Molin At: http://people.tamu.edu/~adalmolin ***This is shared under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 United States License***

1. The Encyclopedia of Life: How realistic is it? Ana Dal Molin ENTO681 Seminar Texas A&M University 23 Feb 2009 This work is licensed under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 United States License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/us/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.

2. 18(2) 2003

3. Why?

4. Imagine an electronic page for each species of organism on Earth, available everywhere by single access on command. Edward O. Wilson

6. species images general information description genetics museums classif. Just a matter of organizing existing information? literature copyright format IUCN Red List BHL

8. Many Internet taxonomy initiatives exist J. Mallet perhaps too many K. Willmott

9. http://www.itis.gov ~483,000 names (Jan 2009) http://www.catalogueoflife.org 1.1 million names (includes LSIDs) (Dec 2008) Compiles several databases, including ITIS, GBIF, sp2000, CBD Redundancy of tools ? http://www.ubio.org Focus on searches http://www.ecoport.org http://www.cbd.int/gti/ From Rio’92 Earth Summit (UN) Several databases (separate programs) http://ispecies.org/ “ iSpecies is a test of E O Wilson's idea of a web page for each species” http://nlbif.eti.uva.nl/bis Results from independent initiatives that use specific software : site inactive! http://www.biodiversitylibrary.org/ 10207 titles 10,000,000 pages (Nov 2008) http://www.gbif.org ~171,400,000 occurrence records (v. 1.2.3)

11. Are we lacking funds? NSF: Biodiversity Surveys and Inventories (BS&I) including support for Planetary Biodiversity Inventories: Mission to an (almost) unknown planet (PBI) NSF: PEET All Species Foundation Summit (Harvard, 2001) Earth Summit (CBD, 1992; RIO+10, 2002) “ Important people jet frequently to international biodiversity conferences in expensive locales, while few improvements in taxonomy are yet evident” (Mallet & Willmott) C. Hine’s copy of “What on Earth” House of the Lords report: flags are mentions to information and communication technologies (in “Systematics as Cyberscience”, MIT, 2008)

13. http://www.organismnames.com (…) a unitary organization (…) and web taxonomy should replace printed taxonomy Taxonomists lack goals that are both realistic and relevant. C. J. Godfray Int J Syst Evol Microbiol + LPSN http://www.bacterio.cict.fr http://www.dsmz.de/bactnom/bactname.htm http://www.ipni.org a.k.a. Index Kewensis

14. Dreams of consumption: GenBank GenBank is frequently referenced as what taxonomists should be doing…

15. However, it is not an exclusive/central resource, not free from redundancy with other DBs. Solution: synchronization. “ Taxonomic information could become much more unitary even under existing codes. GenBank and EMBL did not become primary sources of DNA sequence information by decree .” (Mallet & Willmott)

16. Dreams of consumption: PubMed

17. Is this possible? Metadata Data Metadata repository Name Index Occurrence Index Yellow Pages Regional Atlas Annotation Tools Biosecurity Portal Analysis Tools Products LaSalle, 2008. Atlas of Living Australia, ICE2008 presentation

18. http://www.tdwg.org

20. The fragility of metadata is an important concern because things such as the semantic web rely on conventions on data markup becoming widely adopted and used with care, which, according to Doctorow, will not and cannot happen. Ex. AY281248 - Australia: Gubbata, NSW (GPS: 33 38' 07'', 146 33' 12'' Genbank instructions: degrees latitude and longitude in format "d[d.dd] N|S d[dd.dd] W|E" Translating: Examples from Page, R. http://iphylo.blogspot.com/2008/01/metacrap.html -33° 38' 7.08", +146° 33' 10.80“ IS in Australia Ex. DQ502492 - Nicaragua: Rio San Juan, Near Isla de Diamante (ca. 15 km SE El Castillo on Rio San Juan), 10deg56'N Ex. DQ226041 - /lat_lon="6 28.06'N; 58 37.16'W"

23. Questions 1. How realistic is it to have a web page for every species, including an image database that can ultimately be used in fingerprint-like fashion? 2. What exactly are the objectives behind the EOL, GBIF, and the other initiatives? Are they in fact overlapping? 3. Is this collaboration or: 3a. Unnecessary split of resources? 3b. Adding to the mess of linked data without actual information? 4. Can we learn from the example of other areas? Is our situation that different from astronomy or molecular databases, for example? 5. Do we need to change the way taxonomy is being done? 6. Do we need to change the way we deliver information? What are we doing wrong?