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<p><br />
 
<b>Notes from Nature/iDigBio Hackathon to Further Enable Public Participation in the Online Transcription of Biodiversity Specimen Labels</b>
'''Notes from Nature/iDigBio Hackathon to Further Enable Public Participation in the Online Transcription of Biodiversity Specimen Labels'''
</p><p>December 16–20 at the University of Florida, Gainesville  
 
</p>
December 16–20 at the University of Florida, Gainesville  
<h2> Agenda and Logistics  </h2>
 
<ul><li><a href="https://www.idigbio.org/content/hackathon-enable-public-participation-online-transcription-biodiversity-specimen-labels">Hackathon Advertisement</a>
== Agenda and Logistics  ==
</li><li><a href="https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_Draft_Agenda">Agenda</a>
 
</li><li><a href="https://www.idigbio.org/wiki/images/8/8a/IDigBio_Public_Participation_in_Digitization_Workshop_Logistics_4Dec13.pdf">Logistics Document</a>
*[https://www.idigbio.org/content/hackathon-enable-public-participation-online-transcription-biodiversity-specimen-labels Hackathon Advertisement]
</li><li><a href="https://www.idigbio.org/wiki/images/a/a2/Transcription_Hackathon_Participant_List_8Dec13.pdf">Participants List</a>
*[https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_Draft_Agenda Agenda]
</li><li><a href="http://idigbio.adobeconnect.com/citscribe">AdobeConnect room for planning prior to the hackathon, then for connection to the workshop remotely</a> (Send an email to Austin Mast, if you'd like to use the room for planning prior to the hackathon.)
*[https://www.idigbio.org/wiki/images/8/8a/IDigBio_Public_Participation_in_Digitization_Workshop_Logistics_4Dec13.pdf Logistics Document]
</li></ul>
*[https://www.idigbio.org/wiki/images/a/a2/Transcription_Hackathon_Participant_List_8Dec13.pdf Participants List]
<h2> Coordination  </h2>
*[http://idigbio.adobeconnect.com/citscribe AdobeConnect room for planning prior to the hackathon, then for connection to the workshop remotely] (Send an email to Austin Mast, if you'd like to use the room for planning prior to the hackathon.)
<ul><li><a href="https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_Interoperability_Planning">Interoperability Track</a>
 
</li><li><a href="https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_OCR_Integration_Planning">OCR Integration Track</a>
== Coordination  ==
</li><li><a href="https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_Reconciliation_of_Replicates_Planning">QA/QC and Reconciliation of Replicates Track</a>
 
</li><li><a href="https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_User_Engagement_Planning">User Engagement Track</a>
*[https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_Interoperability_Planning Interoperability Track]
</li><li><a href="https://docs.google.com/document/d/1ns_10ZMBRMOZX1DzfRBdALjhKtr_x8yYaAZLJH6YHyI/edit?usp=sharing">Participants Interest in Tracks</a>
*[https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_OCR_Integration_Planning OCR Integration Track]
</li></ul>
*[https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_Reconciliation_of_Replicates_Planning QA/QC and Reconciliation of Replicates Track]
<h2> Presentations </h2>
*[https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_User_Engagement_Planning User Engagement Track]
<ul><li>Yonggang Liu, iDigBio: <a href="https://docs.google.com/presentation/d/1-R6r_kDnf6IyxSHg1J3M-oRy_wGngLFCwUJg_w4oBAU/edit?usp=sharing">Image Ingestion at iDigBIo</a>
*[https://docs.google.com/document/d/1ns_10ZMBRMOZX1DzfRBdALjhKtr_x8yYaAZLJH6YHyI/edit?usp=sharing Participants Interest in Tracks]
</li><li>Austin Mast, iDigBio: <a href="https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Mast_Lightning_Talk.pdf">Public Participation</a>
 
</li><li>Yun Ling Yim, UC Berkeley: <a href="https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Calbug_idigbio_Jun.pdf">Calbug Digitization, CalBug California Arthropod Collections</a>
== Presentations ==
</li><li>Miao Chen, Indiana U.: <a href="https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/lightningtalk-miaochen.pdf">Using OCR</a>
*Yonggang Liu, iDigBio: [https://docs.google.com/presentation/d/1-R6r_kDnf6IyxSHg1J3M-oRy_wGngLFCwUJg_w4oBAU/edit?usp=sharing Image Ingestion at iDigBIo]
</li><li>Cody Meche, UF: <a href="https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Agile.pdf">Agile Scrum</a>
*Austin Mast, iDigBio: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Mast_Lightning_Talk.pdf Public Participation]
</li><li>Julie Allen, INHS: <a href="https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Allen.pdf">Gamification</a>
*Yun Ling Yim, UC Berkeley: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Calbug_idigbio_Jun.pdf Calbug Digitization, CalBug California Arthropod Collections]
</li><li>Edward Gilbert, Symbiota Developer: <a href="https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Symbiota_2013-12-16.pdf">Symbiota: a specimen-based biodiversity portal platform</a>
*Miao Chen, Indiana U.: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/lightningtalk-miaochen.pdf Using OCR]
</li><li>Deborah Paul, iDigBio Augmenting OCR WG: <a href="https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/aOCRLightning.pptx">What's new in using OCR output in a Citizen Science Workflow</a>
*Cody Meche, UF: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Agile.pdf Agile Scrum]
</li><li>Andrea Matsunaga, iDigBio: <a href="https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/MatsunagaiDigBioCrowdsourcingHackathon2013.pdf">Herbarium Labels Transcription Crowdsourcing &amp; OCR</a>
*Julie Allen, INHS: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Allen.pdf Gamification]
</li><li>Joshua Campbell, iDigBio: <a href="https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/CampbelliDigBioCrowdsourcingHackathon2013.pdf">Herbarium Labels Transcription Crowdsourcing Consensus</a>
*Edward Gilbert, Symbiota Developer: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Symbiota_2013-12-16.pdf Symbiota: a specimen-based biodiversity portal platform]
</li><li>Yonggang Liu, ACIS iDigBio: <a href="https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Yonggang_image_ingestion_appliance.pdf">iDigBio Image Ingestion Appliance</a>
*Deborah Paul, iDigBio Augmenting OCR WG: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/aOCRLightning.pptx What's new in using OCR output in a Citizen Science Workflow]
</li><li>Paul Kimbereley, Smithsonian: <a href="https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/SI_Center.pdf">Smithsonian Transcription Center</a>
*Andrea Matsunaga, iDigBio: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/MatsunagaiDigBioCrowdsourcingHackathon2013.pdf Herbarium Labels Transcription Crowdsourcing & OCR]
</li></ul>
*Joshua Campbell, iDigBio: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/CampbelliDigBioCrowdsourcingHackathon2013.pdf Herbarium Labels Transcription Crowdsourcing Consensus]
<h2> Development Resources  </h2>
*Yonggang Liu, ACIS iDigBio: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Yonggang_image_ingestion_appliance.pdf iDigBio Image Ingestion Appliance]
<ul><li> <a href="https://github.com/idigbio-citsci-hackathon">GitHub organization for this Transcription Hackathon</a>
*Paul Kimbereley, Smithsonian: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/SI_Center.pdf Smithsonian Transcription Center]
</li><li> 4 existing crowdsourcing datasets from Notes From Nature. Datasets contain transcriptions of different types of collections labels. Read more <a href="https://docs.google.com/document/d/1UCz5WblnNIvqBErX-XeWgS9mf69qFhycHqntQOGnPp4/edit?usp=sharing">here</a>. The datasets were shared only with the hackaton participants through dropbox once anonymized. It will be made public when we get a definitive approval from NfN.
 
<ul><li> Calbug dataset
== Development Resources  ==
</li><li> Herbarium labels—The filenames with "USAM_" represent a nearly complete set of recent transcriptions from a collection (the University of South Alabama Herbarium), four replicates for most specimens (I think).
* [https://github.com/idigbio-citsci-hackathon GitHub organization for this Transcription Hackathon]
</li><li> Macrofungi labels
* 4 existing crowdsourcing datasets from Notes From Nature. Datasets contain transcriptions of different types of collections labels. Read more [https://docs.google.com/document/d/1UCz5WblnNIvqBErX-XeWgS9mf69qFhycHqntQOGnPp4/edit?usp=sharing here]. The datasets were shared only with the hackaton participants through dropbox once anonymized. It will be made public when we get a definitive approval from NfN.
</li><li> Ornithological dataset
** Calbug dataset
</li></ul>
** Herbarium labels—The filenames with "USAM_" represent a nearly complete set of recent transcriptions from a collection (the University of South Alabama Herbarium), four replicates for most specimens (I think).
</li></ul>
** Macrofungi labels
<ul><li> Existing solution datasets to assess quality of crowdsourcing consensus (we are working to get "gold standard" data for some of these:
** Ornithological dataset
<ul><li> Herbarium labels ideal response: link to be provided by Austin
 
</li><li> Entomology labels  ideal response: link to be provided by Austin
* Existing solution datasets to assess quality of crowdsourcing consensus (we are working to get "gold standard" data for some of these:
</li><li> Field notebooks  ideal response: link to be provided by Austin
** Herbarium labels ideal response: link to be provided by Austin
</li></ul>
** Entomology labels  ideal response: link to be provided by Austin
</li></ul>
** Field notebooks  ideal response: link to be provided by Austin
<ul><li> For those interested in experimenting with the images that have been used for public participation in transcription:
 
<ul><li> Herbarium label images: the set of ca. 16,000 "USAM" images used for some of the herbarium transcriptions is available at <a href="http://www.specimenimaging.com/images/USAM/">USAM Herbarium Images</a>.  This is several GB worth of image files.  To get them, you could use the DownloadThemAll Firefox plugin.  
* For those interested in experimenting with the images that have been used for public participation in transcription:
</li></ul>
** Herbarium label images: the set of ca. 16,000 "USAM" images used for some of the herbarium transcriptions is available at [http://www.specimenimaging.com/images/USAM/ USAM Herbarium Images].  This is several GB worth of image files.  To get them, you could use the DownloadThemAll Firefox plugin.  
</li></ul>
 
<ul><li> <a href="http://www.notesfromnature.org/">Notes From Nature</a> web interface:
* [http://www.notesfromnature.org/ Notes From Nature] web interface:
<ul><li> Code available at https://github.com/zooniverse/notesFromNature
** Code available at https://github.com/zooniverse/notesFromNature
</li><li> Forked version for the Hackathon available at: https://github.com/idigbio-citsci-hackathon/notesFromNature
** Forked version for the Hackathon available at: https://github.com/idigbio-citsci-hackathon/notesFromNature
</li><li> Install Vagrant from http://downloads.vagrantup.com/tags/v1.3.5 and virtualBox from https://www.virtualbox.org/wiki/Downloads
** Install Vagrant from http://downloads.vagrantup.com/tags/v1.3.5 and virtualBox from https://www.virtualbox.org/wiki/Downloads
</li><li> Vagrant script to build a VM with Notes From Nature web interface:  https://github.com/idigbio-citsci-hackathon/nfn-vagrant
** Vagrant script to build a VM with Notes From Nature web interface:  https://github.com/idigbio-citsci-hackathon/nfn-vagrant
</li><li> Go to the location of the vagrant script and type "vagrant up" in your command prompt to build a VM with Note from Nature running on localhost:9294.
** Go to the location of the vagrant script and type "vagrant up" in your command prompt to build a VM with Note from Nature running on localhost:9294.
</li><li> API Calls
** API Calls
<ul><li> https://api.zooniverse.org/projects/notes_from_nature/groups/
*** https://api.zooniverse.org/projects/notes_from_nature/groups/
</li><li> https://api.zooniverse.org/projects/notes_from_nature/groups/5170103b3ae74027cf000002
*** https://api.zooniverse.org/projects/notes_from_nature/groups/5170103b3ae74027cf000002
</li></ul>
 
</li></ul>
* [[CYWG iDigBio Image Ingestion Appliance]]:
</li></ul>
** The appliance can be used to ingest the images to be used by the crowdsourcing service into the iDigBio storage, and made publicly accessible through HTTP. The relationship between the image filenames and the URL can be exported by the appliance in CSV format.
<ul><li> <a _fcknotitle="true" href="CYWG iDigBio Image Ingestion Appliance">CYWG iDigBio Image Ingestion Appliance</a>:
 
<ul><li> The appliance can be used to ingest the images to be used by the crowdsourcing service into the iDigBio storage, and made publicly accessible through HTTP. The relationship between the image filenames and the URL can be exported by the appliance in CSV format.
* Gold Images from aOCR Hackthon:
</li></ul>
** CSV file with URLs for the Images on iDigBio beta server (Uploaded by Image Ingestion Appliance): [http://www.acis.ufl.edu/~yonggang/idigbio/recordset/gold/ent.csv ent], [http://www.acis.ufl.edu/~yonggang/idigbio/recordset/gold/herb.csv herb],[http://www.acis.ufl.edu/~yonggang/idigbio/recordset/gold/lichens.csv lichens].
</li></ul>
 
<ul><li> Gold Images from aOCR Hackthon:
* Code from the aOCR Hackthon:
<ul><li> CSV file with URLs for the Images on iDigBio beta server (Uploaded by Image Ingestion Appliance): <a href="http://www.acis.ufl.edu/~yonggang/idigbio/recordset/gold/ent.csv">ent</a>, <a href="http://www.acis.ufl.edu/~yonggang/idigbio/recordset/gold/herb.csv">herb</a>,<a href="http://www.acis.ufl.edu/~yonggang/idigbio/recordset/gold/lichens.csv">lichens</a>.
** HandwritingDetection (https://github.com/idigbio-aocr): an algorithm that separates images into sets with no handwriting, little handwriting (mostly text typed or printed), lots of handwriting, based on the noise generated by the OCR software. [http://manuscripttranscription.blogspot.com/2013/02/detecting-handwriting-in-ocr-text.html Read more at Ben's blog]. This could be used to rank which images are in more need for human transcription.
</li></ul>
** Dictionaries to improve crowdsourcing consensus (e.g., names of collectors, scientific names): link to be provided by aOCR?
</li></ul>
*** (Some [http://webprojects.huh.harvard.edu/authority_files/ botantists]: RDF and tab-delimited.)
<ul><li> Code from the aOCR Hackthon:
 
<ul><li> HandwritingDetection (https://github.com/idigbio-aocr): an algorithm that separates images into sets with no handwriting, little handwriting (mostly text typed or printed), lots of handwriting, based on the noise generated by the OCR software. <a href="http://manuscripttranscription.blogspot.com/2013/02/detecting-handwriting-in-ocr-text.html">Read more at Ben's blog</a>. This could be used to rank which images are in more need for human transcription.
 
</li><li> Dictionaries to improve crowdsourcing consensus (e.g., names of collectors, scientific names): link to be provided by aOCR?
* Hi all - (Paul Flemons).
<ul><li> (Some <a href="http://webprojects.huh.harvard.edu/authority_files/">botantists</a>: RDF and tab-delimited.)
**I have uploaded a number of files:
</li></ul>
***https://www.idigbio.org/wiki/index.php/File:OpenRefine_procedures_for_EVENTS_1212a.pdf - a description of Open Refine procedures used for matching BVP fields to EMu EVENTS
</li></ul>
***https://www.idigbio.org/wiki/index.php/File:Preparing_BVP_data_for_import_into_EMu_-_process_1212a.pdf Detailed process of preparing BVP data for EMu
</li></ul>
***https://www.idigbio.org/wiki/index.php/File:Preparing_BVP_data_for_import_into_EMu_-_overview.pdf Overview of preparing BVP data for EMu
<p><br />
***https://www.idigbio.org/wiki/index.php/File:VisioDiagramofProcess.JPG Diagram of the process of preparing data from BVP for EMu
</p>
 
<ul><li> Hi all - (Paul Flemons).
*From Steve Raden: some background on Zooniverse's design
<ul><li>I have uploaded a number of files:
**http://arfon.org/how-the-zooniverse-works-tools-and-technologies
<ul><li>https://www.idigbio.org/wiki/index.php/File:OpenRefine_procedures_for_EVENTS_1212a.pdf - a description of Open Refine procedures used for matching BVP fields to EMu EVENTS
**http://arfon.org/how-the-zooniverse-works-keeping-it-personal
</li><li>https://www.idigbio.org/wiki/index.php/File:Preparing_BVP_data_for_import_into_EMu_-_process_1212a.pdf Detailed process of preparing BVP data for EMu
**http://arfon.org/how-the-zooniverse-works-the-domain-model
</li><li>https://www.idigbio.org/wiki/index.php/File:Preparing_BVP_data_for_import_into_EMu_-_overview.pdf Overview of preparing BVP data for EMu
 
</li><li>https://www.idigbio.org/wiki/index.php/File:VisioDiagramofProcess.JPG Diagram of the process of preparing data from BVP for EMu
== Hackathon Products  ==
</li></ul>
*Brainstorming Documents from the Thursday Mix Ups
</li></ul>
**Group 1 [https://docs.google.com/document/d/1aMVXG3GzTznYBs9R6lQ13Tny_CyBIcMJ_LPLj1zlz7U/edit Mix Up Discussion Summary] (google doc)
</li></ul>
**Group 2
<ul><li>From Steve Raden: some background on Zooniverse's design
**Group 3 [https://docs.google.com/document/d/1B6kvLFw_Mzhrsx4xPgJm29w5j75TpSihdDXFauyt2YM/edit MixUp google doc]
<ul><li>http://arfon.org/how-the-zooniverse-works-tools-and-technologies
**Group 4 [https://docs.google.com/document/d/1-Z-oiwjZZiCh-nVHGZHhUBphY5Z-rcJBnZzn6vnJtBs/edit Mix Up Discussion Summary] (google doc]
</li><li>http://arfon.org/how-the-zooniverse-works-keeping-it-personal
</li><li>http://arfon.org/how-the-zooniverse-works-the-domain-model
</li></ul>
</li></ul>
<h2> Hackathon Products  </h2>
<ul><li>Brainstorming Documents from the Thursday Mix Ups
<ul><li>Group 1 <a href="https://docs.google.com/document/d/1aMVXG3GzTznYBs9R6lQ13Tny_CyBIcMJ_LPLj1zlz7U/edit">Mix Up Discussion Summary</a> (google doc)
</li><li>Group 2
</li><li>Group 3 <a href="https://docs.google.com/document/d/1B6kvLFw_Mzhrsx4xPgJm29w5j75TpSihdDXFauyt2YM/edit">MixUp google doc</a>
</li><li>Group 4 <a href="https://docs.google.com/document/d/1-Z-oiwjZZiCh-nVHGZHhUBphY5Z-rcJBnZzn6vnJtBs/edit">Mix Up Discussion Summary</a> (google doc]
</li></ul>
</li></ul>
<a _fcknotitle="true" href="Category:Transcription_Hackathon">Transcription_Hackathon</a>

Revision as of 16:51, 20 December 2013


Notes from Nature/iDigBio Hackathon to Further Enable Public Participation in the Online Transcription of Biodiversity Specimen Labels

December 16–20 at the University of Florida, Gainesville

Agenda and Logistics

Coordination

Presentations

Development Resources

  • <a href="https://github.com/idigbio-citsci-hackathon">GitHub organization for this Transcription Hackathon</a>
  • 4 existing crowdsourcing datasets from Notes From Nature. Datasets contain transcriptions of different types of collections labels. Read more <a href="https://docs.google.com/document/d/1UCz5WblnNIvqBErX-XeWgS9mf69qFhycHqntQOGnPp4/edit?usp=sharing">here</a>. The datasets were shared only with the hackaton participants through dropbox once anonymized. It will be made public when we get a definitive approval from NfN.
    • Calbug dataset
    • Herbarium labels—The filenames with "USAM_" represent a nearly complete set of recent transcriptions from a collection (the University of South Alabama Herbarium), four replicates for most specimens (I think).
    • Macrofungi labels
    • Ornithological dataset
  • Existing solution datasets to assess quality of crowdsourcing consensus (we are working to get "gold standard" data for some of these:
    • Herbarium labels ideal response: link to be provided by Austin
    • Entomology labels ideal response: link to be provided by Austin
    • Field notebooks ideal response: link to be provided by Austin
  • For those interested in experimenting with the images that have been used for public participation in transcription:
    • Herbarium label images: the set of ca. 16,000 "USAM" images used for some of the herbarium transcriptions is available at <a href="http://www.specimenimaging.com/images/USAM/">USAM Herbarium Images</a>. This is several GB worth of image files. To get them, you could use the DownloadThemAll Firefox plugin.
  • <a _fcknotitle="true" href="CYWG iDigBio Image Ingestion Appliance">CYWG iDigBio Image Ingestion Appliance</a>:
    • The appliance can be used to ingest the images to be used by the crowdsourcing service into the iDigBio storage, and made publicly accessible through HTTP. The relationship between the image filenames and the URL can be exported by the appliance in CSV format.


Hackathon Products

<a _fcknotitle="true" href="Category:Transcription_Hackathon">Transcription_Hackathon</a>

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