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[[Category:Transcription Hackathon]][[Category:Workshop]]
'''Notes from Nature/iDigBio Hackathon to Further Enable Public Participation in the Online Transcription of Biodiversity Specimen Labels'''  
'''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  
December 16–20 at the University of Florida, Gainesville  
{| class="wikitable" style="float:right;"
! colspan="2" style="background:#D58B28;width:200px;font-size:10pt" | Digitizing the Past and Present for the Future
|-
| colspan="2" style="text-align:center;font-size:7pt" | <!--YOU CAN INSERT A NEW IMAGE FOR THE LOGO BETWEEN THE COLON AND THE PIPE-->[[Image:IDigBio Logo RGB.png|center|300px|iDigBio Logo RGB.png]]<br />
|-
!colspan="2" style="background:#D58B28;text-align:center;font-size:9pt" | Quick Links for Transcription Hackathon Workshop
|-
|[https://docs.google.com/document/d/1TyluwM1rMcq7O_nidy8CLJFMW4FrOPjsHkrLVho5cVU/edit?usp=sharing Transcription Hackathon Workshop Agenda]
|-
|[https://www.idigbio.org/biblio?f%5bkeyword%5d=274 Transcription Hackathon Workshop Biblio Entries]
|-
|[https://www.idigbio.org/content/citscribe-hackathon Transcription Hackathon Workshop Report]
|}


== Agenda and Logistics  ==
== Agenda and Logistics  ==


*[https://www.idigbio.org/content/hackathon-enable-public-participation-online-transcription-biodiversity-specimen-labels Hackathon Advertisement]  
*[https://www.idigbio.org/content/hackathon-enable-public-participation-online-transcription-biodiversity-specimen-labels Hackathon Advertisement]  
*[https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_Draft_Agenda Tentative Agenda]  
*[[Transcription Hackathon Draft Agenda| Agenda]]
*[https://www.idigbio.org/wiki/images/8/8a/IDigBio_Public_Participation_in_Digitization_Workshop_Logistics_4Dec13.pdf Logistics Document]  
*[[Media:IDigBio_Public_Participation_in_Digitization_Workshop_Logistics_4Dec13.pdf|Logistics Document]]
*[https://www.idigbio.org/wiki/images/3/33/Transcription_Hackathon_Participant_List_3Dec13.pdf Participants List]  
*[[Media:Transcription_Hackathon_Participant_List_23Dec13.pdf|Participants List]]
*[http://idigbio.adobeconnect.com/citscribe AdobeConnect room for planning prior to the hackathon, then for connection to the workshop remotely]
*[http://idigbio.adobeconnect.com/citscribe AdobeConnect room for collaboration after the hackathon, then for connection to the workshop remotely] (Send an email to Austin Mast, if you'd like to use the room for additional collaboration after the hackathon.)


&nbsp; &nbsp;&nbsp;Send an email to Austin Mast, if you'd like to use the room for planning prior to the hackathon.
== Media ==
*[https://www.facebook.com/media/set/?set=a.645283388848944.1073741833.215120891865198&type=1 Citscribe Hackathon Facebook Album]
*Twitter stuff: @iDigBio @NfromN hashtag #CITScribe
 
==Report==
*[https://www.idigbio.org/content/citscribe-hackathon Citscribe Hackathon Report]


== Coordination  ==
== Coordination  ==


*[https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_Interoperability_Planning Interoperability Track]  
*[[Transcription Hackathon Interoperability Planning| Interoperability Track]]
*[https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_OCR_Integration_Planning OCR Integration Track]  
*[[Transcription Hackathon OCR Integration Planning| OCR Integration Track]]
*[https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_Reconciliation_of_Replicates_Planning QA/QA and Reconciliation of Replicates Track]  
*[[Transcription Hackathon Reconciliation of Replicates Planning| QA/QC and Reconciliation of Replicates Track]]
*[https://www.idigbio.org/wiki/index.php/Transcription_Hackathon_User_Engagement_Planning User Engagement Track]
*[[Transcription Hackathon User Engagement Planning| User Engagement Track]]
*[https://docs.google.com/document/d/1ns_10ZMBRMOZX1DzfRBdALjhKtr_x8yYaAZLJH6YHyI/edit?usp=sharing Participants Interest in Tracks]
 
== Presentations ==
*Yonggang Liu, iDigBio: [https://docs.google.com/presentation/d/1-R6r_kDnf6IyxSHg1J3M-oRy_wGngLFCwUJg_w4oBAU/edit?usp=sharing Image Ingestion at iDigBIo]
*Austin Mast, iDigBio: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Mast_Lightning_Talk.pdf Public Participation]
*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]
*Miao Chen, Indiana U.: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/lightningtalk-miaochen.pdf Using OCR]
*Cody Meche, UF: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Agile.pdf Agile Scrum]
*Julie Allen, INHS: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Allen.pdf Gamification]
*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]
*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]
*Andrea Matsunaga, iDigBio: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/MatsunagaiDigBioCrowdsourcingHackathon2013.pdf Herbarium Labels Transcription Crowdsourcing & OCR]
*Joshua Campbell, iDigBio: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/CampbelliDigBioCrowdsourcingHackathon2013.pdf Herbarium Labels Transcription Crowdsourcing Consensus]
*Yonggang Liu, ACIS iDigBio: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/Yonggang_image_ingestion_appliance.pdf iDigBio Image Ingestion Appliance]
*Paul Kimberly, Smithsonian: [https://www.idigbio.org/sites/default/files/workshop-presentations/citscribe/SI_Center.pdf Smithsonian Transcription Center]
*William Ulate, Missouri Botanical Garden: [[Media:Purposeful_Gaming_BHL_Dec_2013.pdf|Purposeful Gaming and BHL]]


== Development Resources  ==
== Development Resources  ==
* [https://github.com/idigbio-citsci-hackathon GitHub organization for this Transcription Hackathon]
* 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 hackathon 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 crowdsourcing datasets from Notes From Nature: datasets with transcriptions of different types of collections labels:
* For those interested in experimenting with the images that have been used for public participation in transcription:
** Herbarium labels: link to be provided by NfN or Austin
** 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.
** Entomology labels: link to be provided by NfN or Austin
** Field notebooks: link to be provided by NfN or Austin
 
* Existing solution datasets to assess quality of crowdsourcing consensus:
** 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


* [http://www.notesfromnature.org/ Notes From Nature] web interface:
* [http://www.notesfromnature.org/ Notes From Nature] web interface:
** Code available at https://github.com/zooniverse/notesFromNature
** Code available at https://github.com/zooniverse/notesFromNature
** Forked version available at: link to be provided by Alex
** Forked version for the Hackathon available at: https://github.com/idigbio-citsci-hackathon/notesFromNature
** Vagrant script to build a VM with Notes From Nature web interface: link to be provided by Alex
** 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://virtualbox.org/wiki/Downloads
** Vagrant script to build a VM with Notes From Nature web interface:  https://github.com/idigbio-citsci-hackathon/nfn-vagrant
** 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.
** API Calls
*** https://api.zooniverse.org/projects/notes_from_nature/groups/
*** https://api.zooniverse.org/projects/notes_from_nature/groups/5170103b3ae74027cf000002


* [[CYWG iDigBio Image Ingestion Appliance]]:
* [[CYWG iDigBio Image Ingestion Appliance]]:
** 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.
** 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:
** 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].
* Code from the aOCR Hackthon:
* Code from the aOCR Hackthon:
** 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.
** 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.
** Dictionaries to improve crowdsourcing consensus (e.g., names of collectors, scientific names): link to be provided by aOCR?
** Dictionaries to improve crowdsourcing consensus (e.g., names of collectors, scientific names): link to be provided by aOCR?
*** (Some [http://webprojects.huh.harvard.edu/authority_files/ botantists]: RDF and tab-delimited.)
* Hi all - (Paul Flemons).
**I have uploaded a number of files:
***[[Media:OpenRefine_procedures_for_EVENTS_1212a.pdf|a description of Open Refine procedures used for matching BVP fields to EMu EVENTS]]
***[[Media:Preparing_BVP_data_for_import_into_EMu_-_process_1212a.pdf|Detailed process of preparing BVP data for EMu]]
***[[Media:Preparing_BVP_data_for_import_into_EMu_-_overview.pdf|Overview of preparing BVP data for EMu]]
***[[Media:VisioDiagramofProcess.JPG|Diagram of the process of preparing data from BVP for EMu]]
*From Steve Raden: some background on Zooniverse's design
**http://arfon.org/how-the-zooniverse-works-tools-and-technologies
**http://arfon.org/how-the-zooniverse-works-keeping-it-personal
**http://arfon.org/how-the-zooniverse-works-the-domain-model
== Hackathon Products  ==
*Brainstorming Documents from the Thursday Mix Ups
**Group 1 [https://docs.google.com/document/d/1aMVXG3GzTznYBs9R6lQ13Tny_CyBIcMJ_LPLj1zlz7U/edit Mix Up Discussion Summary] (google doc)
**Group 2
**Group 3 [https://docs.google.com/document/d/1B6kvLFw_Mzhrsx4xPgJm29w5j75TpSihdDXFauyt2YM/edit MixUp google doc]
**Group 4 [https://docs.google.com/document/d/1-Z-oiwjZZiCh-nVHGZHhUBphY5Z-rcJBnZzn6vnJtBs/edit Mix Up Discussion Summary] (google doc)
*Some groups used the Coordination pages above to summarize products
*Group 1 [[Target File Format]]

Latest revision as of 15:35, 3 February 2015


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

Digitizing the Past and Present for the Future
iDigBio Logo RGB.png

Quick Links for Transcription Hackathon Workshop
Transcription Hackathon Workshop Agenda
Transcription Hackathon Workshop Biblio Entries
Transcription Hackathon Workshop Report


Agenda and Logistics

Media

Report

Coordination

Presentations

Development Resources

  • GitHub organization for this Transcription Hackathon
  • 4 existing crowdsourcing datasets from Notes From Nature. Datasets contain transcriptions of different types of collections labels. Read more here. The datasets were shared only with the hackathon 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
  • 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 USAM Herbarium Images. This is several GB worth of image files. To get them, you could use the DownloadThemAll Firefox plugin.
  • CYWG iDigBio Image Ingestion Appliance:
    • 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:
    • CSV file with URLs for the Images on iDigBio beta server (Uploaded by Image Ingestion Appliance): ent, herb,lichens.
  • Code from the aOCR Hackthon:
    • 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. Read more at Ben's blog. This could be used to rank which images are in more need for human transcription.
    • Dictionaries to improve crowdsourcing consensus (e.g., names of collectors, scientific names): link to be provided by aOCR?

Hackathon Products

  • Some groups used the Coordination pages above to summarize products
  • Group 1 Target File Format
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