Writing The Encyclopedia Of Life (not EoL.org)
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A presentation given at the Stockholm Biodiversity Informatics course on 16th Sept. 2009
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Writing The Encyclopedia Of Life (not EoL.org)
- 1. Vincent S. Smith Writing the Encyclopedia of Life
- 5. Taxonomic effort Bacteria 9021 Spp Archaebacteria 259 Spp. Plants 260k spp. Animals 1.18 M spp. Other 193k spp. Fungi 101k 1.8 million species
- 6. Taxonomic effort Crusta- ceans 39k Birds 10k Reptiles 7.1k Mammals 5k Amphib .5k Sponges 10k Cnidarians 9k Rotifers 1.8k Flatworms 13.7k Insects 0.82 M spp. Molluscs 117 k Fish 25k Bacteria 9021 Spp Archaebacteria 259 Spp. Plants 260k spp. Animals 1.18 M spp. Other 193k spp. Fungi 101k 1.8 million species
- 7. Taxonomic effort Crusta- ceans 39k Birds 10k Reptiles 7.1k Mammals 5k Amphib .5k Sponges 10k Cnidarians 9k Rotifers 1.8k Flatworms 13.7k Insects 0.82 M spp. Molluscs 117 k Fish 25k Bacteria 9021 Spp Archaebacteria 259 Spp. Plants 260k spp. Animals 1.18 M spp. Other 193k spp. Fungi 101k Beetles 370k spp. Flies 85k spp. Butterflies & moths 165k spp. Bees, wasps & ants 198k spp. 0.01 papers per species per year i.e 1 paper every 100 years Birds: 1 paper per species per yr. Mammals: 2 papers per species per yr. Elephants: 47 papers per species per yr. 1.8 million species
- 16. Technology moves fast! Technical issues 2 Platforms
- 18. Technical issues 3 Web services (integration hacks)
- 24. Social issues 5 Human Computer Interactions
- 29. What is a Scratchpad? A website for you & your community Your data 1 Published & reviewed on your site 3 Uploaded & tagged 2
- 30. What is a Scratchpad? A website for you & your community Your data 1 Published & reviewed on your site 3 Uploaded & tagged 2 Fast Intuitive Fit for use
- 31. What can Scratchpads do? Import, manage, search & browse: DNA & Phylogenies Literature Specimens Images
- 32. DNA & Phylogenies Specimens Literature Images What can Scratchpads do? Integration & connectivity within & between sites Taxonomy
- 33. +Administration -Change your site information -Change you front page -Change your logo -Activity and access logs +Backup -Backing up your data -Restoring your data +Bibliography -Creating a record -Importing from a ref. manager -Exporting to a reference manager +Blog -Creating and adding a blog +Custom Content -Defining a CCK -Importing from a spreadsheet -Creating a custom view +Fileshare -Creating and using a fileshare +Forum -Altering the forum settings -Creating a container for a forum -Creating a new forum -Creating a new topic inside a forum +Groups -Creating a group -Subscribing to a group +Image -Uploading & basic annotation -Linking image & location records -Linking image & specimen records -Linking image & publication records -Overlay annotations on images +Layout -Change your theme -Menus -Blocks and sidebars +Locations -Creating a record -Importing from a spreadsheet +Pages -Creating, editing, cloning & deleting -Configuring the panels template +Panels -Adding & configuring content -Creating a new panel -Citing a Panels page +Phylogeny -Adding a phylogenetic tree +Specimens -Creating a record -Importing from a spreadsheet -Linking specimen & location records -Linking specimen & pub. records +Tasks -Creating a tasklist +Taxonomy -Importing from a spreadsheet -Importing from ClassificationBank -Starting from scratch -Taxonomy manager -Displaying a classification -Adding names -Deleting names -Taxonomy & panels +Users -Your settings -Adding a new user -User roles and permissions -Adding and editing user profile fields -Logging in +Webform -Creating and using webforms What can Scratchpads do? In summary:
- 34. What can Scratchpads do? Visual taskguide
- 35. Current Scratchpads Ants Bees Beetles Big-headed flies Birds Blackflies Ciliates Cockroaches Dragon Trees Dung Beetles False Buttonweed Flat worms Flies Foraminifera Fossil Insects Fungus Gnats Holometabola Leaf-miner Flies Lice Lichens of Bermuda Malvaceae Megalastrum ferns Milichiid flies Mosquitoes Mosses Nannotax fossils Nepticuloid moths Palms Pearl oysters Polychaete worms Scaleworms Termites Triticid grasses Weevils Wood Ferns Sulawesi Ferns Stick insects Sites: 130+ Users: 1500+ Pages: 170k Since March 2007
- 36. Scratchpad applications A multipurpose, flexible technology 4th Edition Howard & Moore, Birds of the world ( fact checking, data compilation, 2010, funding ) eBooks
- 37. European Mosquito Bulletin (ISSN 1460-6127), Phasmid Studies (ISSN 0966-0011) ( submission, review, & dissemination of articles ) eJournals Scratchpad applications A multipurpose, flexible technology
- 38. Image galleries Nanno fossils, Cockroaches, Stick insects, Flatworms, Grasses, Lichens & many more… ( rapid upload, annotation, & display of images ) Scratchpad applications A multipurpose, flexible technology
- 39. GBIF, Zootaxa, Threatened Plants of the World (Kew), BarCoVer (DNA Barcoding) & more ( space for data collection, services, discussion, & organization ) Societies & Organizations Scratchpad applications A multipurpose, flexible technology ZOOTAXA A rapid international journal for animal taxonomists ISSN 1175-5326 (Print Edition) & ISSN 1175-5334 (Online Edition)
- 42. Autotagging Indexing data to make it findable 1. Create content 2. Find terms 3. Submit (Index) (Autotag) (e.g. reference) Journal citation mentions taxon name
- 43. 1. Create content 2. Find terms 3. Submit (Index) (Autotag) (e.g. reference) Autotagging Indexing data to make it findable Matches taxonomy term (Drag & Drop)
- 44. 1. Create content 2. Find terms 3. Submit (Index) (Autotag) (e.g. reference) Autotagging Indexing data to make it findable Page tagged (indexed) with taxon name
- 46. Integrating data & “publishing” in a Scratchpad How do Scratchpads work? Types of Scratchpad Panel… Taxonomic hierarchies Files and documents Phylogenetic trees Customized content Specimen records Photographs & illustrations Personalized instructions Common names Bibliographic literature Built with “tagged data”
- 47. Dynamically built species pages Integrating data & “publishing” in a Scratchpad How do Scratchpads work?
- 48. Browsed through a taxonomy Integrating data & “publishing” in a Scratchpad How do Scratchpads work?
- 49. Including 3 rd party content Integrating data & “publishing” in a Scratchpad How do Scratchpads work?
- 50. With data curation tools Integrating data & “publishing” in a Scratchpad How do Scratchpads work?
- 51. Listing all “authors” Integrating data & “publishing” in a Scratchpad How do Scratchpads work?
- 52. Dated, permanent & citable Integrating data & “publishing” in a Scratchpad How do Scratchpads work?
- 53. Choose which panels to display Adjusting the panels layout How do Scratchpads work?
- 54. An example based on the Catalogue of Life classification How do Scratchpads work? 2 million taxon pages Open curation at http://catlife.myspecies.info
- 55. Questions?
- 57. Scratchpad management Scalable & sustainable technology Virtual machine, open-source software, self-archiving, backed-up, multi-site configuration ( easy to move & upgrade, secure & reliable, citable, screencasts, low admin., low marginal costs ) Hardware, software & user support
Editor's Notes
- The mission - to describe and document the diversity of life Inventory the Earth’s species Document their relationships “ Publish” these data
- Problems with the current model Bias in what we are work on - taxonomy is parochial, requires specialists
- NHM Struggled to find someone describing a new species for DC2.