Collecting quantitative metadata by counting all specimens in a herbarium

6f6914b1cdb438695ec1aaabba7463bb?s=47 Peter Desmet
October 18, 2011

Collecting quantitative metadata by counting all specimens in a herbarium

Talk at the TDWG 2011 annual conference in New Orleans, United States - October 18, 2011.

What information do you get when you count all specimens in a herbarium?

6f6914b1cdb438695ec1aaabba7463bb?s=128

Peter Desmet

October 18, 2011
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Transcript

  1. Collec&ng   quan&ta&ve  metadata   by  coun&ng  all  specimens  in

     a   herbarium   Peter   Desmet  
  2. Quan&ta&ve  metadata  are  cool!   A  very  colourful  presenta&on  by

      @peterdesmet  #tdwg  
  3. Index  Herbariorum   350,000,000   herbarium  specimens  worldwide  

  4. 25,000,000   digi&zed  and  published  (=  7%)   GBIF  Data

     Portal  (Andrea  Hahn)  
  5. What  do  we  know  about  the  other   93%  ?

     
  6. Descrip&ve   metadata  

  7. Metadata  registries   bit.ly/IH-­‐herbaria   biocol.org  

  8. Collec&on  name  +  code   Address   Staff   Subcollec&ons

     
  9. Es&mated  size   Based  on  what?   Actually  counted?  

  10. Geographic  scope   Pre^y  well  described   How  distributed?  

  11. Taxonomic  scope   Vascular  plants  +  Bryophytes?   Families?  

    Genera?  
  12. Can  we  get  some  real  numbers?  

  13. Vascular  plants  specimens   are  organized  in   Folders  

  14. None
  15. None
  16. None
  17. None
  18. What  if  we  counted  the  folders?  

  19. And  the  #  of  specimens  per  folder?  

  20. ?  $   How  much  would  it  cost?  

  21. ?  days   How  long  would  it  take?  

  22. What  we  did  at  the   Marie-­‐Victorin   Herbarium  (MT)

     
  23. Move  an  es&mated  900,000  specimens  

  24. More  space   Reassign  350  -­‐>  640  cases  

  25. New  classifica&on   Flowering  plants:  APG  III  (2009)   Ferns:

     Smith  et  al.  (2006)  
  26. Coun&ng   Digi&zing   Data  cleaning   Publishing  

  27. Coun&ng  

  28. None
  29. Average  age  >  60  

  30. None
  31. 1  summer  

  32. 826  work  hours   110  work  days,  22  work  weeks

     
  33. Digi&zing  

  34. 4  volunteers  

  35. Paper  -­‐>  Excel  

  36. Data  cleaning  

  37. 2  volunteers   1  professor   1  informa&cian  

  38. Correc&ng  errors   Typos,  missed  genera,  dubious  counts  

  39. New  classifica&on   Assigning  families,  correc&ng  genera  

  40. Format  data  

  41. Publishing  

  42. 1  informa&cian   (me)  

  43. Google  Fusion  Tables   bit.ly/mt-­‐inventory-­‐gk  

  44. Darwin  Core  Archive  via  IPT   bit.ly/mt-­‐inventory  

  45. Metadata  =  EML   Descrip&ve  metadata  

  46. Occurrence  dataset   basisOfRecord  =  PreservedSpecimen  

  47. 1  record   1  folder   1  genus   1

     loca&on   in  1  tray  
  48. #  specimens   individualCount  

  49. What  do  we   know  now?  

  50. 22,298   folders  

  51. 628,664   specimens  

  52. 2/3   of  previous  es&mate  

  53. 21.5%   digi&zed  

  54. 380   families  

  55. 82%   of  known  families  

  56. 5,298   genera  

  57. 6   con&nents  

  58. Combina&ons   Rubus  specimens  from  Canada?   Yes:  2921,  in

     trays  A236-­‐07  –  A238-­‐04    
  59. Useful  for  us   In-­‐house  management  &  planning   Digi&za&on

     priori&es  
  60. Useful  for  others?   Loans   Demand  driven  digi&za&on?  

  61. Granularity   Genus,  con&nent  -­‐>  Useful  for  climate   change

     &  invasive  species  studies?  
  62. Global  picture   Really  350  mil.  specimens?   How  distributed

     over  genus  &   con&nent?  
  63. Cost  /  Time  ?  

  64. 158   work  days   Publishing  1%   Data  cleaning

     21%   Digi&zing  8%   Coun&ng  70%  
  65. 5,740  $   total  salary  cost   Publishing  7%  

    Digi&zing  0%   Coun&ng  37%   Data  cleaning  56%  
  66. 110  specimens  =  1$   100  &mes  cheaper  than  full

     digi&za&on  
  67. 3,200,000  $   All  350  mil.  specimens  

  68. 138  h     1049  h   Staff  5,740  $

      Volunteers  0  $   88%  by  volunteers  
  69. 16,230  $   10$  wage  for  “volunteers”  +  staff  salary

     
  70. 9,000,000  $   All  350  mil.  specimens  

  71. 340  years   1  person  at  7.5h/day,  5  days/week,  no

      holidays  
  72. 26  days   One  person  per  herbarium   3,400  herbaria

     -­‐  Index  Herbariorum  
  73. ?!   Tricky  to  extrapolate!   What  about  non-­‐mounted  specimens?

      How  useful  is  this  data?   Is  there  a  metadata  repository?  
  74. First  step   Towards  some  real  numbers  

  75. Thanks!   bit.ly/mt-­‐inventory   Peter   Desmet