Field to Database: Difference between revisions

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 |[https://www.idigbio.org/wiki/index.php/Field_to_Database#Agenda Field to Database Workshop Agenda]
 |-
-|Field to Database Workshop Biblio Entries
+|[https://www.idigbio.org/biblio?f%5bkeyword%5d=460 Field to Database Workshop Biblio Entries]
 |-
-|Field to Database Workshop Report (Workshop Blog)
+|[https://www.idigbio.org/content/rmarkdown-github-reproducible-research Field to Database Workshop Report (Workshop Blog)]
 |}
 [[Category:Workshop]][[Category: Data carpentry]][[Category: Biodiversity informatics]]
-<div>This Wiki supports the short course - Field to Database: Biodiversity Informatics and Data Management Skills for Specimen Based Research. Where? The University of Florida at iDigBio from March 9 - 12, 2015. It is the third in a series of four biodiversity informatics workshops planned in collaboration with the [http://tcn.amnh.org/ Tri-Trophic Thematic Collection Network] for iDigBio in the upcoming year (2014-2015). The fourth workshop in this series is Sept 15-16, 2015 and focuses on Data Management for Collection Managers.</div>
+<div>This Wiki supports the short course - Field to Database: Biodiversity Informatics and Data Management Skills for Specimen Based Research. Where? The University of Florida at iDigBio from March 9 - 12, 2015. It is the third in a series of four biodiversity informatics workshops planned in collaboration with the [http://tcn.amnh.org/ Tri-Trophic Thematic Collection Network] for iDigBio in the upcoming year (2014-2015). The fourth workshop in this series is Sept 15-16, 2015 and focuses on [https://www.idigbio.org/wiki/index.php/Managing_Natural_History_Collections_Data_for_Global_Discoverability Data Management for Collection Managers].</div>
 == Apply Now ==
@@ Line 104: / Line 104: @@
 ===Workshop Evaluation===
-* link to pre-workshop survey (if we do one)
+* Our pre-workshop survey simply asked participants to rank their R skills. With 19 respondents, our participants formed a heterogenous group:
-* Post Workshop Survey Results
+** 6 chose "Low. I am a total beginner, have no or little experience, or have only gone through the R tutorial."
+** 5 chose "Somewhat low. I have used R, but only under the guidance of someone more expert (e.g., during a course or workshop)."
+** 5 chose "Neither high nor low. I can use and adapt scripts written by other people."
+** 3 chose "Somewhat high. I can write my own scripts."
+* [[Media:F2dbfinalsurvey.pdf|Post Workshop Survey Results for Field to Database]]
 ==Agenda==
@@ Line 124: / Line 128: @@
 |-
 |830 - 850
-|[https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/IntroAndLogisticsF2DBiDigBio.pptx Welcome and Introduction to iDigBio.] (pptx)<br/>[https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/F2DB%20PSoltis.pptx Motivation = Research!] (pptx)([https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/F2DB%20PSoltis.pdf pdf version])
+|[https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/IntroAndLogisticsF2DBiDigBio.pptx Welcome and Introduction to iDigBio.] (pptx)<br/>[https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/F2DB%20PSoltis.pptx Motivation = Research! (pptx)][https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/F2DB%20PSoltis.pdf (pdf)]
 |Deb Paul (iDigBio) &<br/> Pam Soltis (iDigBio PI)
 |-
 |850 - 910
-|Why a Field-to-Database Biodiversity Informatics Workshop? [https://www.dropbox.com/sh/crmaz7smc3w8qmf/AACe83xbxgDY_i6NisH7vVXma?dl=0 R_files_modeling]
+|[https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/DataCarpentryCharlotte.pptx Why a Field-to-Database Biodiversity Informatics Workshop? (pptx)]([[Media:DataCarpentryCharlotte.pdf|pdf]])<br/>[https://www.dropbox.com/sh/crmaz7smc3w8qmf/AACe83xbxgDY_i6NisH7vVXma?dl=0 R_files_modeling]
 |Charlotte Germain-Aubrey (iDigBio Post Doc) and Katja Seltmann (TTD-TCN)
 |-
@@ Line 136: / Line 140: @@
 |-
 |930 - 940
-|How to prioritize where you collect? How do you plan a collecting trip? What kind of resources do you bring in the field?
+|[[Media:IDigBio_FieldworkPlanning_F2DB.pdf|Using Digital Resources to Plan Field Expeditions]]<br/>How to prioritize where you collect? How do you plan a collecting trip? What kind of resources do you bring in the field?
 |Grant Godden
 |-
 |940 - 1000
-|Field templates, workflow, and planning ahead for better results.
+|[https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/iDigBioWorkshopTalk_SHORT.pdf Tips and Workflows for Managing Field Data]<br/>Field templates, workflow, and planning ahead for better results.
 |Andrew Short
 |-
 |1000 - 1010
-|Collecting RNA, DNA & flower color. Lessons from a recent field trip.
+|[[Media:IDigBio_GenomicResources_F2DB.pdf| Standards for Collection of Genomic Resources]]<br/>Collecting RNA, DNA & flower color. Lessons from a recent field trip.
 |Grant Godden
 |-
@@ Line 156: / Line 160: @@
 |-
 |1110 - 1130
-|Top 10 mobile applications every biologist should know about. Download and try.
+|Top 10 mobile applications every biologist should know about. Download and try. Here are some.
+*Compass [https://itunes.apple.com/us/app/commander-compass-lite/id340268949?mt=8 Commander Compass Lite]
+*Random Number Generator: [https://play.google.com/store/apps/details?id=com.brandao.randomnumbergenerator&hl=en Generate Random Numbers App]
+*Range Finder/Height Measurements: [https://play.google.com/store/apps/details?id=kr.sira.measure&feature=search_result#?t=W251bGwsMSwyLDEsImtyLnNpcmEubWVhc3VyZSJd Smart Measure]
+*Epicollect: for Dataforms http://www.epicollect.net/<br/>
+*Sound Recording:
+**Free: [https://itunes.apple.com/us/app/audionote-lite-notepad-voice/id379301403?mt=8 AudioNote Lite - Notepad and Voice Recorder]
+**Pay: [https://itunes.apple.com/us/app/irecorder-pro-audio-recorder/id285750155?mt=8 iRecorder Pro - Audio Recorder] (Pay) Or
+***[https://itunes.apple.com/us/app/voice-recorder-hd/id373045717?mt=8 Voice Recorder HD for Audio Recording, Playback, Trimming and Sharing]
+*OPTIONAL BUT USEFUL FOR MANY
+**Light: [https://itunes.apple.com/us/app/geotag-photos-lite/id374252911?mt=8 Geotag Photos Lite]
+***PAY: Geotagging Photos: [https://itunes.apple.com/us/app/geotag-photos-pro/id355503746 Geotag Photos Pro]
 |Emilio Bruna
 |-
@@ Line 168: / Line 183: @@
 |-
 |1200 - 1230
-|Brown bag lunch discussion. Standards: Darwin Core and more. Emphasis of benefits of starting off using them right away. Presented in field using a handout and conversation regarding Darwin Core and other standards. Input from outside experts important for addressing sound/image/paleontological and ecological standards. Metadata.<br />[http://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/DarwinCoreStandardsHandoutV2.docx Field Handout - 1) Summary of some relevant standards including: Darwin Core, Ecological Metadata Language (EML), Audubon Media Extension, Global Genome Biodiversity Network (GGBN) and 2) Best practices for writing a locality description].
+|Brown bag lunch discussion. Standards: Darwin Core and more. Emphasis of benefits of starting off using them right away. Presented in field using a handout and conversation regarding Darwin Core and other standards. Input from outside experts important for addressing sound/image/paleontological and ecological standards. Metadata.<br />[http://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/DarwinCoreStandardsHandoutV2.docx Field Handout] - 1) Summary of some relevant standards including: Darwin Core, Ecological Metadata Language (EML), Audubon Media Extension, Global Genome Biodiversity Network (GGBN) and 2) Best practices for writing a locality description.
 |Deb Paul
 |-
@@ Line 176: / Line 191: @@
 |-
 |100 - 330
-|'''Breakout Group 1''': Activity (60min): Students are grouped into pairs or groups of three. Each team does two rounds of mini-collecting, 10 minutes each for total of 20 minutes. For the first 10 min: Each team has to collect and record data for a few insects they collect on blank paper (e.g. a journal page). For the second 10 minutes, each team repeats this process but now is given a generic data sheet to fill in. The collecting focus is insects on plants.
+|'''Breakout Group 1''': Activity (60min): Students are grouped into pairs or groups of three. Each team does two rounds of mini-collecting, 10 minutes each for total of 20 minutes. For the first 10 min: Each team has to collect and record data for a few insects they collect on blank paper (e.g. a journal page). For the second 10 minutes, each team repeats this process but now is given a generic data sheet to fill in. The collecting focus is insects on plants.<br/>
+[[Media:FLworkshopDataSheet.pdf|Sample Field Data Collection Sheet]]<br/>
+[[Media:FLworkshopFieldLabels.pdf|Sample Field Labels]]
 |Andrew Short & Grant Godden
 |-
@@ Line 210: / Line 227: @@
 |-
 |900 - 940
-| Fossil field collection and field site 3D reconstruction including present paleo databases and standards.
+|[[Media:JustinWoods-iDigBio-March2015.pdf|Fossil field collection and field site 3D reconstruction including present paleo databases and standards.]]<br/>[https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/Excavation%20Instructional%20iDigBio.mp4 Excavation Instructional Video]
 | Justin Woods
 |-
 |940 - 1000
-| Efficient workflow from collection to cataloging for marine invertebrates.
+|[[Media:Field-methods.pdf|Efficient workflow from collection to cataloging for marine invertebrates.]]
 | François Michonneau
 |-
@@ Line 238: / Line 255: @@
 |-
 |1:30-5:00
-| Getting started with R
+|[http://idigbio.github.io/2015-03-09-workshop-field2db/intro-R.html Getting started with R]
 | François Michonneau (Lead)
 |-
@@ Line 291: / Line 308: @@
 |9:00-12:00
 |Using R to access biodiversity APIs
-*9-930 Explanation of API & packages (Matt)
+*9:00-9:30 Explanation of API & packages (Matt)<br/>
-*930-1000 Installation of packages in R including installing needed packages (Francois)
+[[Media:2015-03-12-F2DB-Apis.pdf|Introduction to Web APIs]]
-*1000-1020 Break
+*9:30-10:00 Installation of packages in R including installing needed packages (Francois)
-*1020-1200 Working with APIs using packages (Matt)
+*10:00-10:20 Break
+*10:20-12:00 Working with APIs using packages (Matt)<br/>
+[[Media:2015-03-12-F2DB-R_pkg_lesson.pdf|Using APIs in R]]<br/>
+[https://raw.githubusercontent.com/iDigBio/2015-03-09-workshop-field2db/gh-pages/r_pkg_lesson.R R Script for lesson]
 |Francois Michonneau, Matt Collins (Leads)
 |-
@@ Line 306: / Line 326: @@
 |-
 |2:30-4:00
-|Publishing data on Dryad (includes discussion of metadata)
+|[https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/vision_field2db_march2015.pdf  Publishing data on Dryad]
 |Todd Vision, Dryad (http://datadryad.org) (Lead)
 |-
@@ Line 344: / Line 364: @@
 :#[https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/Collecting.pptx Field to Freezer: Low tech collecting; high quality data.] Shelley James, Herbarium Pacificum, Bishop Museum
 :#[https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/Specify%20for%20field%20data.mp4 From the Field Into Specify: several options.] (mp4) Andrew Bentley, Specify, University of Kansas Biodiversity Institute<br/>[https://www.idigbio.org/wiki/index.php/Specify_6_Appliance_Download_and_Installation Installation Package for Specify]
-:#From the Field Into Symbiota
+:#From the Field Into Symbiota<br/>Part 1: [http://idigbio.adobeconnect.com/p9hep7duj96/ Field Reach perspective] (time: 10:20) – Show how a field research can enter a voucher specimen along with a field image, link voucher to a checklist, and print labels to be distributed with the specimen vouchers.<br/>Part 2: [http://idigbio.adobeconnect.com/p68flaqagcg/ Curator’s perspective] (time: 11:05) – Shows how a curator can import a record from the collector’s data set to their own collection rather than retyping the label data from scratch. Also includes how identification annotations can filter down the network of specimen duplicates to correct a misidentification within the original checklist.
-::Part 1: [http://idigbio.adobeconnect.com/p9hep7duj96/ Field Reach perspective] (time: 10:20) – Show how a field research can enter a voucher specimen along with a field image, link voucher to a checklist, and print labels to be distributed with the specimen vouchers.
-::Part 2: [http://idigbio.adobeconnect.com/p68flaqagcg/ Curator’s perspective] (time: 11:05) – Shows how a curator can import a record from the collector’s data set to their own collection rather than retyping the label data from scratch. Also includes how identification annotations can filter down the network of specimen duplicates to correct a misidentification within the original checklist.
 :#Digitally archiving localities through the use of their coordinates. Amy Smith, Collections Manager of Earth Sciences, Perot Museum of Nature and Science<br/>[https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/ACS_GoogleMaps.avi Digitally visualizing and archiving coordinates using KML files]<br/>[https://www.idigbio.org/sites/default/files/workshop-presentations/field-to-database/ACS_GoogleMaps.pdf PDF to accompany video]
 :#[https://vimeo.com/107473692 Filling Biodiversity Knowledge Gaps] (GBIF video) Dr Arturo Ariño discusses potential information gaps that exist between different sources of data, using two case studies the UN Biosphere Reserves in Mexico and Spain.
@@ Line 355: / Line 373: @@
 :[http://ropensci.org/tutorials/taxize_tutorial.html taxize tutorial]
 :[https://github.com/ropensci/taxize taxize on github]
-:[https://github.com/fmichonneau/ridigbio ridigbio]
+:[https://github.com/idigbio/ridigbio ridigbio]
 :[https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs Open Tree of Life APIs]
 :[https://github.com/VertNet/webapp/wiki/Introduction-to-the-VertNet-API Introduction to the VertNet API]
@@ Line 410: / Line 428: @@
 ====Day2 ====
 *9:00am-11:00am http://idigbio.adobeconnect.com/p2p6ezjdwdo/
-*11:30pm-12:30pm http://idigbio.adobeconnect.com/p7woy8hro5x/
+*11:30am-12:30pm http://idigbio.adobeconnect.com/p7woy8hro5x/
 *1:30pm-2:30pm http://idigbio.adobeconnect.com/p96rvexycsl/
 *1:45-5:00pm http://idigbio.adobeconnect.com/p5l1dc47t1p/
@@ Line 417: / Line 435: @@
 *9:00-12:30 http://idigbio.adobeconnect.com/p21s71147nh/
 *1:30-3:30 http://idigbio.adobeconnect.com/p6ipnr4eh4v/
-*3:45-5
+*3:45-5 http://idigbio.adobeconnect.com/p8fha4j15ex/
 ====Day4====
-*9:00-12:00
+*9:00-10:30 http://idigbio.adobeconnect.com/p9b106642l6/
-*1:00-2:30
+*11:15-12:15 http://idigbio.adobeconnect.com/p285w4uu5xr/
-*2:30-4:00
+*1:30-2:30 http://idigbio.adobeconnect.com/p30irmqksq8/
-*4:00-5:00
+*2:30-5:00 http://idigbio.adobeconnect.com/p7kabi2d68f/
 ==Related Workshop Resources and Links==