Eol Shorthouse

Sep 10, 2008Download as PPT, PDF0 likes294 views

The document discusses plans for a Drupal taxonomy code sprint to improve how Drupal handles hierarchical taxonomies, large vocabularies, and term reconciliation. It notes challenges with multiple taxonomies, permissions, search integration, and semantic web applications. Participants will submit code patches to Drupal and participate in a Google Code project. Back-porting solutions to D5 is discussed. Examples like the Encyclopedia of Life and biology sites using workarounds are provided, with EOL's taxon-centric approach and LifeDesk profiles outlined. Taxonomy management is highlighted as important for projects like EOL and term reconciliation.

Drupal Taxonomy Code Sprint Why? How well does Drupal currently handle hierarchical taxonomies What about multiple & extremely large vocabularies? What about reconciliation (synonymy, relatedness)? What about machine tagging? What about Semantic Web? Can we hook permissions/roles into selection of terms? How well will our solutions integrate with search?

Best Practices Google Code: Need a Google account https://code.google.com Drupal CVS Patches: tag ��EOL Taxonomy Sprint��

Who & Why You are leading this sprint & you will take ownership of where we take it You will submit patches to Drupal��s CVS You will participate in Google Code svn We want to see D6 & D7 lead the way for CMS�� but many sites continue to make use of D5 Can we push for core solutions that can be back-ported? Can we push for flexible solutions that cut through idiosyncratic needs? Can we develop or refactor existing modules if we cannot pave the way to development in core?

The Encyclopedia of Life David P. Shorthouse Vitthal Kudal

Biology-Centric, Drupal Solutions BugGuide Are not using taxonomy or views ScratchPads Use taxonomy as a mechanism to tag content with scientific names Many biological pursuits have chosen other CMS�� or Drupal workarounds ( e.g. Animal Diversity Web)

EOL Approach - Drupal Major participatory thrust: Drupal multisites (eventually standalone) called LifeDesks Three profiles: Expert, Citizen Scientist, K-12 December release: taxa-centric , LifeDesk: Expert Each have capacity to build ��species pages��: Contents of which are atomized as nodes (e.g. chapters of text, images, videos, specimens, etc.) for storage Aggregated for HTML representation (View? Template? Panel?) Each must produce an XML document using schema just as do existing biodiversity website partners http://lifedesk.eol.org

Taxonomy Management Immensely important for the success of EOL��s LifeDesks, EDIT��s ScratchPads, and other biology-centric pursuits Editor is paramount to success Reconciliation of terms is critical Drag & drop functionality between terms and synonyms & differentiation among kinds of synonyms ( i.e. objective synonym, subjective synonym, common name, language of common name)

Canadensys is a network of 11 universities, 2 botanical gardens, and 2 museums that aims to mobilize 3 million specimen records (20%) by the end of 2013. The network standardizes biodiversity data using tools like narwhal-processor and integrates a publishing toolkit to generate metadata and map data to DarwinCore standards. It uses a geospatial stack including PostGIS, ElasticSearch, and Windshaft to make searchable data available through a web application. The network seeks to reconcile scientific names by mapping names among classifications and addressing issues like synonyms, homonyms, and inconsistent nomenclature.

ShorthouseDavid Shorthouse

The document discusses the Encyclopedia of Life (EOL) project, which aims to create a web page for every known species containing key information about it. It outlines EOL's goals of aggregating biodiversity data from various sources and making it openly accessible online. The document also describes EOL's efforts to establish a taxonomic framework and infrastructure to facilitate collaborative curation of species pages.

10minutes RogerDavid Shorthouse

This document discusses managing taxonomy data for biodiversity projects. It provides background on previous work using Drupal to manage taxonomy for various education projects. It describes issues with using the taxonomy.module to manage taxonomy, including handling synonyms, common names, ranks, and authorship. It also discusses how the ADW taxonomy was built from multiple sources and how taxonomy data could be better managed in the future by separating source data and building composite classifications to import into other databases.

Global Names ievobio 2012David Shorthouse

This document discusses global scientific naming and the need to recognize and resolve scientific names to their current usage. It introduces tools and a pipeline to find, atomize, index, resolve, and edit scientific names from various data sources on a global scale. These tools are available on various websites and through open-source code on GitHub to facilitate consistent naming across scientific literature and databases.

Have We Got the Names "Right"?David Shorthouse

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The document discusses key trends in social media and mobile for 2013, including the rise of mobile social platforms like Facebook and Twitter and increased content creation and sharing on mobile. It also outlines strategies for organizations to develop optimized social media programs, including aligning programs with objectives, using various engagement tactics, and developing community management best practices. The goal is to leverage paid, owned, and earned social media to amplify messaging and drive engagement through an integrated converged media approach.

GlobalNames - Canadensys - ShorthouseDavid Shorthouse

This document discusses Global Names Recognition and Discovery (GNRD), a high throughput system for extracting scientific names from documents. GNRD uses multiple name-finding engines like NetiNeti and TaxonFinder to extract names from text and OCR'd documents. It outputs the names and their locations in JSON/XML format. Over 15,000 OCR'd articles from 1868-2002 were processed by GNRD, extracting 158,000 unique scientific names. The document also discusses using Darwin Core terms for taxonomic name searches and representations. It provides examples of biodiversity databases like AntWeb and VASCAN that implement taxonomic name search using Darwin Core terms. Suggestions are made for AntCat to also adopt similar

BSC Shorthouse ESC 2011David Shorthouse

The document discusses the development of an online checklist journal called the Biological Survey of Canada that would serve as a bottom-up, structured yet flexible platform for compiling taxonomic information on Canadian species. It would include both human-readable manuscripts and machine-readable supplemental data archives. The goal is to make the information purposeful, reusable and engaging for both human and machine consumption. Support is needed to champion this initiative and help secure funding to realize this vision.

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What do accessible occurrence data and checklists tell us about species diver...David Shorthouse

This document discusses accessible occurrence data and checklists in Canada and what they can tell us about species diversity. It notes that over 11 million occurrence records are available on GBIF from Canada. While these data are accessible, many records have outdated taxonomy or lack location coordinates. The document encourages making checklist data openly available but notes it requires curation. Opportunities for innovative research using these biodiversity data are mentioned.

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Eol Drupal Dman PresentationDavid Shorthouse

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Eol Shorthouse

1. Drupal Taxonomy Code Sprint Why? How well does Drupal currently handle hierarchical taxonomies What about multiple & extremely large vocabularies? What about reconciliation (synonymy, relatedness)? What about machine tagging? What about Semantic Web? Can we hook permissions/roles into selection of terms? How well will our solutions integrate with search?

2. Best Practices Google Code: Need a Google account https://code.google.com Drupal CVS Patches: tag ��EOL Taxonomy Sprint��

3. Who & Why You are leading this sprint & you will take ownership of where we take it You will submit patches to Drupal��s CVS You will participate in Google Code svn We want to see D6 & D7 lead the way for CMS�� but many sites continue to make use of D5 Can we push for core solutions that can be back-ported? Can we push for flexible solutions that cut through idiosyncratic needs? Can we develop or refactor existing modules if we cannot pave the way to development in core?

4. The Encyclopedia of Life David P. Shorthouse Vitthal Kudal

5. Biology-Centric, Drupal Solutions BugGuide Are not using taxonomy or views ScratchPads Use taxonomy as a mechanism to tag content with scientific names Many biological pursuits have chosen other CMS�� or Drupal workarounds ( e.g. Animal Diversity Web)

6. EOL Approach Content aggregated from other biodiversity websites using client-produced XML docs Schema produced in-house using existing (Dublin Core) and emerging standards (TDWG: Species Profile Model) Front-end: Ruby on Rails Back-end: MySQL

7. Schema for Data Objects

8. EOL Approach - Drupal Major participatory thrust: Drupal multisites (eventually standalone) called LifeDesks Three profiles: Expert, Citizen Scientist, K-12 December release: taxa-centric , LifeDesk: Expert Each have capacity to build ��species pages��: Contents of which are atomized as nodes (e.g. chapters of text, images, videos, specimens, etc.) for storage Aggregated for HTML representation (View? Template? Panel?) Each must produce an XML document using schema just as do existing biodiversity website partners http://lifedesk.eol.org

9. Taxonomy Management Immensely important for the success of EOL��s LifeDesks, EDIT��s ScratchPads, and other biology-centric pursuits Editor is paramount to success Reconciliation of terms is critical Drag & drop functionality between terms and synonyms & differentiation among kinds of synonyms ( i.e. objective synonym, subjective synonym, common name, language of common name)

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