A great shout-out to our volunteers!

An article was just published which highlights the wonderful work that our volunteers have been doing.

It is called Citizen Volunteers Pitch in on Digitization Backlog and is in the journal BioScience. Once again a sincere thanks for the enormous efforts of our volunteers!

Updated FAQ and Useful tools: Herbarium Interface

The following is an updated FAQ that includes the topics covered in our first Notes From Nature FAQ post (http://blog.notesfromnature.org/2014/04/17/faqs-and-useful-tools/). We are most thankful to our dictated volunteers who made great suggestion to improve and clarify some important issues. The discussion and suggestions can be found here: http://talk.notesfromnature.org/#/boards/BNN0000003/discussions/DNN00003mc

Note that this FAQ only covers issues related to the herbarium interface (SERNEC). We will be developing specific FAQs for all the Notes From Nature interfaces over the coming months.

1.) Interpretation: In general, you should minimize interpretation of open-ended fields and enter information verbatim. This way, we can better achieve consensus when checking multiple records against one another (see below, on that process). However, some discretion would be nice. Here are examples:

Interpretation that you should make: Simple spacing errors (e.g. “3miN. of Oakland” should be “3 mi N. of Oakland”)

Interpretation you should leave to us: Don’t interpret abbreviations, we’ll sort that out. (e.g. “Convict Lk.” )

2.) Not in English: Transcribe exactly as written. Match label content to transcription fields as best as you can. Non-English labels should be rarely encountered in the herbarium interface, but may occasionally occur.

3.) Abbreviations: Transcribe exactly as written.

4.) Spelling mistakes: Transcribe exactly as written, unless you have looked it up and are absolutely certain of a simple spelling mistake. In this case, you can enter the correct spelling.

5.) Problem records: If you come across a problem record that may need to be addressed by a scientist, like a faulty image or a record with illegible handwriting, you can flag the record by commenting on it (e.g. with the hashtag #error) and indicate what is in error. Note that the hash tag #scientist is also frequently used for this purpose.

6.) Provinces: Geographic provinces (e.g. Coastal Plain, Piedmont) should go into the Location field.

7.) Capitalization: Sometimes information may be in all capital letters on the labels. Unless this is an abbreviation, you should capitalize only the first letter of every word in your transcription (e.g. “COASTAL PLAIN PROVINCE” should be “Coastal Plain Province”).

8.) Many collectors: In many cases, collectors may be listed on different lines of the label with no punctuation separating them. In your transcription, please separate the collectors with commas.

9.) Missing information: What should you do when there is no information available for a field? When information is not given on the label, you should leave the field blank (in the case of open-ended fields) or select “Unknown” or “Not Shown” in the drop-down lists

10.) Inconsistent collector names: You will often find several variations of the same collector name (e.g. “R. Kral” or “R.Kral”, “RWG” or “R.W.Garrison”). We are asking for the collector names to be typed as written. This is a somewhat complicated issue since same collectors might appear to be very similar but aren’t always the same. It can take know a lot of about the collector and where they deposited specimens to be able to make a definitive decision.

Interpretation that you should make: Simple spacing errors (e.g. “R.Kral” should be “R. Kral”)

Interpretation you should leave to us: Don’t interpret abbreviations, we’ll sort that out. (e.g. “RWG” should remain “RWG”)

11.) Many scientific names: For SERNEC Herbarium specimens, copy only the most recent name. This can be determined based on the date that appears on the ‘annotation label.’ If you do not see a date then enter the name that appears on the primary label.

When the latest determination uses an abbreviation for the genus name, because the genus is the same as the previous/original determination, the genus name should be written out in full. Examples: http://talk.notesfromnature.org/#/subjects/ANN0003mbn , http://talk.notesfromnature.org/#/subjects/ANN0003jz1

The “determination label” or later added determination information should have everything spelled out, however this is not always the case. If the first letter is the same it is safe to assume the same genus is being used. For example, J. marginatus would = Juncus marginatus and “Juncus” would be written out.

12.) Varieties and subspecies: Record the subspecies, but omit the scientific author’s name. So “Cyperus odoratus var. squarrosus (Britton) Jones, Wipff & Carter” becomes “Cyperus odoratus var. squarrosus”. “Echinodorus cordifolius (Linnaeus) Grisebach ssp. cordifolius” becomes “Echinodorus cordifolius ssp. cordifolius”.

13.) Scientific name: Provide the most recent name, whether it is a species name (a two-word combination of the genus and what is called the “specific epithet” in botanical nomenclature) or a one-word name that is at a higher taxonomic rank (e.g., just the genus or family name). Names at higher taxonomic ranks than species are used when a more precise identification has not been made.  The species name should typically take the form of a genus name that begins with a capital letter and a specific epithet that begins with a lowercase letter.  If any of the names are given in all capitals, such as “CYPERUS ODORATUS”, the name should be entered using the typical convention, “Cyperus odoratus” in this case.

14.) Latitude and Longitude: How do you enter latitude and longitude values, and where do these values go? Enter exactly as written, you can find symbols in Word or by searching online (e.g. 33° 62’ 22” N  116° 41’ 42” W). You can also produce the degree symbol ° using key combinations (alt + 0 on a mac; alt + 0176 on a PC, with the key pad on the right side of your keyboard). This information should go into the “Location” field.

15.) Special Characters: What should you type when there is a special character in a text string, such as a degree symbol or language-specific characters? You can do a google search for the symbol or copy and paste it from Microsoft Word symbols. There are also key combinations for common symbols. As mentioned above, you can produce the degree symbol ° using key combinations (alt + 0 on a mac; alt + 0176 on a PC, with the key pad on the right side of your keyboard).

16.) Elevation: Enter elevation verbatim into the “Habitat and Description” field.

17.) County: If the county is not given on the label, please find the appropriate county using google search or other tools highlighted below. However, if there are multiple potential counties for a locality, please leave the county field blank.

18.) Checking your transcription: You can use the link to the left of the “Finish Record” button (e.g. “1/9” or “9/9”) to check the information that you entered. Just click on any of the fields to make any necessary edits to your transcription.

19.) When is a record finished?: These blog posts describe the data checking process that uses 4 transcriptions of the same record to derive a consensus.

http://blog.notesfromnature.org/2014/01/14/checking-notes-from-nature-data/

http://soyouthinkyoucandigitize.wordpress.com/2014/01/14/412/

20.) Question: Should powerlines go in the location (because it helps you find a place), or habitat (because they imply a more open space and different microclimate)? Example: http://talk.notesfromnature.org/#/subjects/ANN0003qbt

Answer:

This should go in the Habitat field. It could help narrow down a location, but it says more about habitat where the plant was growing.

21.) Question: What do you enter when a record has two different counties? Example: http://talk.notesfromnature.org/#/subjects/ANN000412e

Answer:

This doesn’t happen very often. It usually indicates that the collector wasn’t entirely sure which county they were in e.g. at the boundary between the two. When you encounter this, I would suggest going with the first county listed.

I did do a bit of sleuthing and in this case I think the collectors were trying to indicate that they were on the county line. The Flint River does have a road crossing near the Spalding / Fayette County line.

22.) Question: What do you enter when a record has two different dates?

Answer:

You should enter the first date only. This is also very uncommon on herbarium label so we chose to collect only one date.

23.) Question: On this record, would you rather have the scientific name as ‘unidentified’ or as the supposition? http://talk.notesfromnature.org/#/subjects/ANN0003ynx

Answer:

This is a tough one! I can tell that the original collector (Carter) and the annotator (Kral) agree that it is in the genus Rhynchospora, but they just can’t get any further than that. Ideally you would just enter “Rhynchospora”, but leaving it blank (skipping it) would be acceptable. If the scientific name is blank or can’t be figured out then it should be skipped.

24.) Question: If “s.n.” (sine numerum = no number) is listed as the Collector Number, is it better to leave the field empty or actually put “s.n.” in it?

Answer:

It is recommend to leave it blank, since ideally we would just have actual numbers in that field. Also many people – experts and non-experts – don’t know what s.n. refers to.

25.) Question: Should “floodplain” be in Habitat? I’m inclined to put it there as it describes a growing condition as floodplains are fertilized when flooded, other plants drowned, etc.

Answer:

Yes, please put it into the habitat field.

26.) Question: What is the convention for transcribing a date range as opposed to one specific day? (ie first, last or midway through the range)

Answer:

Enter the first date only. See also #22 above.   It is worth noting the conventions in other collecting disciplines is to take a range of dates (e.g. insects and CalBug) but it isn’t for herbarium specimens.

27.) Question: If a specimen is cultivated at one location from cuttings/seeds/rhizomes collected at a second location, which should be the transcribed country/state/county/location, the first or second?

Answer:

Enter the place where it was actually collected. In this case the cultivated place. I haven’t seen the label, but it is likely a good idea to indicate the cultivated information in the habitat field.

28.) Question: Although we transcribe only the latest determination if there are multiple, should we also transcribe multiple synonyms in the same determination if they are listed, or just the first? (ie “Cyperus echinatus [=C. ovularis]”)

Answer:

No. There is no need to add the synonyms, just enter the first or primary name. In this case “Cyperus echinatus.”

29.) Question: Should we also transcribe multiple collector numbers as written? ie “123 & 4567″ (Probably an obvious “yes” but isn’t formally in the Standards.)

Answer:

This could indicate that each collector gave the specimen a number in the field. This is an uncommon practice and even when it happens it doesn’t go on the same label. In this case, I suggest entering it exactly as is.

30.) Question: Should we transcribe location information that is printed into the template of the label rather than being added? (such as “Plants of the Great Dismal Swamp” or “Flora of Fort…” etc.)

Answer:

This is a bit of a judgment call, but in general the answer is yes if it is not indicated elsewhere. For example you often see “Plants of North Carolina” and the state is also indicated as North Carolina. In this case, the template really doesn’t give us any new information and it should not be entered. One should also be careful of institutional templates. For example, “Herbarium of Florida State University, Tallahassee.” Labels could have the name of a museum in Florida, but the specimen could be collected in Virginia.

31.) Question: Should we transcribe “Collected as part of a survey…” and other info that doesn’t relate to this specimen per se?

Answer:

No. We do not expect you to transcribe this information. While it is interesting and potentially important we are also interested in keeping the process efficient and not overly time consuming.

32.) Question: Should we transcribe “sheet # of #” or other information indicating that this specimen is part of a set, but again is not just about this one per se?

Answer:

No. We do not expect you to transcribe this information.

33.) Question: Should we transcribe re-examination? ie “This specimen was examined as part of a study of…” that occurs years after the original label.

Answer:

No. This is part of a series of information that relates to annotations of the specimens. It is not considered to be core information that we are trying to collect.

34.) Question: Should we transcribe personal comments that clearly have nothing to do with the specimen? (Thinking Philip E. Hyatt here for some reason).

Answer:

No. See #33 above which covers a similar issue. But if you find something awesome, interesting, etc. please post it in the talk forum!

35.) Question: If a word is hyphenated across two lines, do we remove the hyphen and join it? (Not including hyphenated word pairs of course. This is probably also an obvious “yes” but should be in the Standards formally.)

Answer:

Yes, please remove the hyphen.

36.) Question: Should we transcribe Habitat/Description (or other specimen-relevant) info in later, separate determinations? (sometimes the person who made it adds a comment with further info about the specimen, i.e. its condition or maturity.)

Answer:

Yes. If the annotation clearly contains information added by the collector that fits into one of the fields then add it.

 

Some Useful Tools (discovered or developed by Notes From Nature users)

Counties and Cities: Good tools for finding counties etc. are lists on wikipedia, there are lists of municipalities in each state of the USA (there are also similar lists for others). For example, https://en.wikipedia.org/wiki/List_of_municipalities_in_Florida (via the linkbox you can also change the state).

Mountains: https://en.wikipedia.org/wiki/Category:Lists_of_mountains_of_the_United_States

Uncertain Localities: Geographic Names Information System, U.S. Geological Survey.

https://geonames.usgs.gov/pls/gnispublic

Mapping tool with topo quads: To find uncertain counties or localitieshttp://mapper.acme.com

Collector Names: Harvard University Herbarium maintains a database of collectors (http://kiki.huh.harvard.edu/databases/botanist_index.html). Note that many collectors that are encountered may not be in this database.

Hard-to-read text: Use “Sheen”, the visual webpage filter, for some hard-to-read handwriting written in pencil. (Tip was from the War Diary Zooniverse project) https://chrome.google.com/webstore/detail/sheen/mopkplcglehjfbedbngcglkmajhflnjk?hl=en-GB

Special symbols: You should be able to find symbols in word or by doing a google search and copy and paste. Here are a few:

– degree symbol for coordinates:  °

– plus minus: ±

– fractions: ⅛ ¼ ⅓ ⅜ ½ ⅝ ⅔ ¾ ⅞

– non-English symbols: Ä ä å Å ð ë ğ Ñ ñ õ Ö ö Ü ü Ž ž

The Plant List: Search for scientific names of plants – http://www.theplantlist.org/

List of Trees: https://en.wikipedia.org/wiki/Category:Trees_of_the_United_States

Integrated Taxonomic Information System (ITIS): http://www.itis.gov/

Mr Kevvy’s has generated a very useful set of custom dictionaries. They can be found here:

http://www.baldurdash.org/Herbarium&MacrofungiWordListDictionary5.1.zip

These dictionaries are a wonderful resource. It should be noted that scientific names can have gender based differences. You will see the specific epithet (commonly called the “species name”) with male and female genera spellings. An example albiflora is feminine and albiforus is masculine. The Carolina-poppy is Argemone albiflora (not albiflorus). Both albiflora and albiflorus are correctly spelled, but in this case albiflorus should never be used with the genus Argemone.

Simultaneous Transcription Blitzes a Success!

This is a cross-post with iDigBio and authored by Austin Mast, Richard Carter, and Libby Ellwood.

On Saturday, March 28, from 8–noon 31 volunteers gathered in computer labs at Valdosta State University (participants shown above) and Florida State University (participants shown to left) for a transcription blitz benefiting the VSU Herbarium and FSU’s Robert K. Godfrey Herbarium.  The blitz used two online transcription platforms: Zooniverse’sNotes from Nature and the Botanical Society of Britain and Ireland’s Herbaria@home.  In the end, 1748 transcriptions were completed—an average of 56 per person for the 4-hour event. This was the second in what is planned to be a series of digitization blitzes ocoordinated by iDigBio, the Southeastern Regional Network of Expertise and Collections Thematic Collections Network, and FSU’s Robert K. Godfrey Herbarium.  The FSU images that were transcribed had been generated during the first of these, an imaging blitz in September 2014.  Prizes and event-branded thank-you gifts for the blitz were paid for by the contributors to the successful December 2014 crowdfunding campaign by FSU’s herbarium. Richard Carter (VSU), Austin Mast (FSU) and Libby Ellwood (FSU) served as local organizers.

Each location began the blitz with a 30-minute introduction to the local herbarium and the importance of specimens to research and education, as well as an orientation to the transcription platform.  After
participants gained familiarity with the procedure, the organizers introduced one of four games that they used to prompt the participants to think more deeply about what they were seeing in the specimen images.  These games included Habitat Bingo (shown on right), Morphology Bingo, Timeline Tracker, and Geo Locator, which required participants to use habitat terms, morphology, collection dates, and collection localities, respectively.  The organizers introduced a new game every hour, and small prizes were given out to multiple winners for each game.  FSU also ran a raffle for a native blueberry plant, and transcribers received one raffle ticket for every five specimens transcribed.  The remaining prizes were raffled off as well at the end of the event.  Organizers provided a coffee break midway through the event.

In FSU’s formal post-event survey, 60% of participants reported a greater familiarity with biodiversity research specimens and their use in research and education; 100% agreed or strongly agreed that
biodiversity research collections merit public funding; and 73% strongly agreed that they enjoyed the transcription blitz and would participate again.  The most popular game was Geo Locator, with 87% finding it enjoyable or very enjoyable; each of the other games were enjoyed by 67% or more of the participants.  Half of the FSU participants had not visited FSU’s Robert K. Godfrey Herbarium in the past; 67% had not transcribed specimen labels previously; and 67% had not previously participated in a citizen science project.  VSU ran an informal post-event survey, and VSU’s participants particularly liked the bingo games. We do not yet have long-term data on the “stickiness” of the experience, but we know that at least two participants continued transcribing specimens online in the first 24 hours after the blitz.

Organizers learned a few lessons with this first transcription blitz.  First, the event produced progress in digitization for the herbaria and built community support for the collections.  Second, the event was easier to host than FSU’s 2014 imaging blitz, since it only required access to computers and browser software to do the digitization on the day of the event, rather than relatively complicated imaging stations.  Third, both transcription platforms were dependable—we engaged two in case of technical difficulties with one during the event (e.g., if high traffic led to a server crash).  However, orienting the group to the second one mid-morning took time away from transcribing.  It would be most efficient to just use one platform and hold the other as a backup.  Fourth, the games were a high point for many of the participants and did not result in any drop in the rate of transcription relative to online, distributed participants.  In fact, onsite participants had a higher rate of transcription.

Herbarium transcriptions on Notes from Nature average 3.65 minutes per specimen when done by distributed participants, and, if one takes into account the 45 minutes used for orientation and break, onsite participants averaged 3.48 minutes per specimen.  Fifth, orienting them to each new game took time away from transcribing.  Two games played over a longer period would have fit more comfortably into the schedule.  Sixth, a few subjects are critical for the training: the parts to a scientific name and what should be entered (e.g., should the author or varietal name be included), what an annotation label represents, how to identify the extent of a habitat description and a locality description, and the meaning of “s.n.”  And finally, there is room for development of more structurd interactions between simultaneous events.  The two computer labs were projected onto the screen (shown to right) and participants waved to each other, but otherwise activities at the two sites were independent of one another.

Development of these cross-site interactions will become more important with the Worldwide Engagement for Digitization of Biocollections (WeDigBio) event planned for October 2015.  WeDigBio has the goal of recruiting organizers for dozens of these events during a four-day period.  The next transcription blitz at FSU will be in conjunction with the Florida Native Plant Society annual meeting on Friday, May 29, from 8–noon.

Success!

lemur success kid

Lemur success kid

This week Notes From Nature achieved an amazing milestone. Our volunteers transcribed a huge set of herbarium images. This set contained over 50,000 specimen images from two museum collections in the southeast United States. The collections are from Florida State University and Valdosta State University. Both of these collections are part of a broader initiative to digitize museum specimens from the biologically rich southeast United States (sernec.org). The resulting dataset will represent a valuable resource for research. This research will inform areas such as the response of vegetation to global change, human development, and rapid migrations of introduced species, just to name a few!

We want to acknowledge this amazing feat and thank our dedicated volunteers for their efforts. We are truly humbled and impressed by your contributions. You rock!

We will have more images coming soon and look forward to future successes. As one of volunteers recently stated, transcribing these specimens will have a lasting impact on our knowledge of biodiversity.

Thank you!

This one is for the birds

The bird ledgers at the Natural History Museum London stretch back over 250 years, and for those of you who have helped do over 319,000 (and counting) transcriptions of items from those ledger, you probably can tell just how old the specimens are just from the handwriting. The science team at Notes from Nature have also puzzled over those ledger entries, even for some of the more careful penmanship. We also know how amazing many of you are at solving the sometimes challenging puzzles found in these ledgers. Its an enormous collection and tremendous job that you are helping to accomplish.

The bird ledgers also have proven to be an adventure in citizen science development — it has required a new type of interface, and some different thinking about how to measure effort.  At the end of 2014, we finally got counting working per row of the ledger, which is somewhat equivalent to a specimen record for other collections in Notes From Nature.  Now we have set it up so we can count your individual row-by-row effort and offer you some rewards for completing work on these ledgers.

We are therefore pleased to announce three new bird badges, which you can acquire when you complete transcription work on the Ornithology collections.   While working on an individual ledger page, you won’t see your badges earned until you hit “Next Ledger” — at that point, you should see the badge you earned show up both in the transcription interface and in your profile page.

nest
You get this badge for transcribing one Ornitological record

fledgling
You get this badge for transcribing 25 Ornithological records

adult
You get this badge for transcribing 200 Ornithological records

This data really is for the birds – for understanding their past distributions and diversity, all in service of better understanding the future of this amazing, diverse and often inspiring group of animals with whom we share this planet.

A special collection of bird ledgers now available on Notes from Nature

Notes from Nature is excited to make available a special new set of Ornithology ledgers!  They are available now and are from one of the true pioneers in our understanding of birds in India, Nepal, Pakistan and other nearby regions.  We are also fortunate to have an expert on that pioneer, Allan Octavian Hume, to tell us more about him.  Below,  Robert Prys-Jones has written more about this amazing early naturalist, whose collections ledger records at the Natural History Museum London are now available to you to help digitize!

Allan Octavian Hume 

Allan Octavian Hume (1829-1912) was responsible for presenting to the NHM the largest bird collection it has ever received, approaching 65,000 bird skins and 20,000 eggs, very largely from the former British India (i.e. modern India, Nepal, Pakistan, Bangladesh, Sri Lanka and Myanmar). However, he was a most extraordinary person in many other ways also. Starting out as a young administrator in the East India Company in 1849, he was officiating magistrate in Etawah, N.W. Provinces, at the time of the Indian Mutiny in 1857, playing a heroic but humane role in pacifying his area of responsibility, in recognition of which he was awarded the Companion of the Order of the Bath (CB). During his subsequent rise through the ranks of the British Raj to hold one of its most senior posts from 1871 to 1879, as Secretary of the Department of Revenue, Agriculture and Commerce, he dazzled with his efficiency but upset some of his superiors through his conviction that the core of his role was not to raise revenue but to improve the lives of ordinary Indian people. Eventually his outspoken views resulted in his demotion, followed by his subsequent retirement at the end of 1881.

These 20 years from the early 1860s to the early 1880s, ones of massive and increasing work responsibility, were when almost the entirety of Hume’s ornithological contribution was made, strictly as a consuming hobby. Gradually building up a network of correspondents and specimen contributors (his “coadjutors”) spanning British India, he made it his aim to transform knowledge of the region’s avifauna. Facilitating this, he published relentlessly, notably in a journal Stray Feathers that he founded and produced, employed a professional bird curator and collector (William Davison) from the early 1870s and mounted major expeditions to poorly-known areas.

Hume’s resignation from the British Raj coincided with his own diminishing interest in ornithology, something exacerbated by his deep but relatively brief involvement with Theosophy at this time, during which he became both a vegetarian and increasingly unwilling to procure specimens in the name of science. At the same time, now unconstrained by his job, his involvement with radical politics blossomed: he played a seminal role in the founding of the Congress Party, which would eventually become the main vehicle of the Indian independence movement and was the party of government in independent India as recently as a couple of years ago. Following the tragic theft of most of his text for his long-planned magnum opus on the Birds of British India, in 1885 Hume donated his entire bird collection to the Natural History Museum and withdrew from ornithology.

Finally returning to live permanently in Britain in 1894, he threw himself into liberal politics, as well as taking up British botany with the documentary zeal he had once devoted to Indian ornithology. Dissatisfied with convenience of access to the Natural History Museum botany collections for the interested working man, his final major act, in 1910, was to set up and endow the South London Botanical Institute (SLBI): over one hundred years later this is still going strong. Meanwhile, his ornithological collection remains the bedrock for all future south Asian bird research, as is fulsomely acknowledged by the most recent handbook for the area (Rasmussen & Anderton 2012 Birds of South Asia. 2 vols. 2nd ed.). In 2012, the centenary year since his death, the NHM and SLBI jointly acknowledged his significance by devoting a one-day conference to him.

Those interested to learn more of Hume may wish to look at a recent review of his life, focused on his ornithology – http://orientalbirdclub.org/wp-content/uploads/2012/11/Allan-Octavian-Hume.pdf – and at the account of him on Wikipedia –  http://en.wikipedia.org/wiki/Allan_Octavian_Hume . The current effort to crowd-source his bird registers will feed directly into on-going research into understanding his development as an ornithologist and into interpreting the science in some of his diaries now held by the NHM.

Irena puella Hume 15 Aug 2012
6 Asian Fairy-bluebirds Irena puella from the Hume collection
_________________________________________________________________

The content about Allan Octavian Hume was written by Robert Prys-Jones and intro. and posting of this by Robert Guralnick.

The Sitch with the Stitch—The CITStitch Hackathon

This is being cross-posted with iDigBio, and co-authored with Libby Ellwood and Austin Mast.

SAMSUNG CAMERA PICTURES

Internet-scale public engagement in the digitization of biodiversity research specimens, such as can be seen at Notes from Nature, DigiVol, the Smithsonian’s Transcription Center, and FromthePage.com, offers clear win-wins insofar as motoring through our 100’s-of-millions-of-specimens digitization backlog and advancing science literacy. However, developing that level of engagement presents some large cyberinfrastructure challenges, given that the community of public engagement tools has yet to interoperate “seamlessly” amongst themselves and with the more established biodiversity data platforms, such as Symbiota and iDigBio. This observation was first widely discussed at iDigBio’s 2012 Public Participation in Digitization of Biodiversity Research Specimens Workshop, which led to iDigBio’s development of Biospex, a prototype public participation project management system.

For the second year in a row, iDigBio and Notes from Nature co-organized a citizen science (CITSCI) hackathon focused on the cyberinfrastructure gaps. You can read about last year’s CITSCribe Hackathon here. The main goal of this year’s CITStitch Hackathon (Dec 3–5) was to build interoperability among projects that enable public participation in digitization in useful and exciting ways for both the public participation project managers and the public participants. Among this year’s 24 participants were developers, data managers and publishers from public participation tools as well as those who work with cool tools for data visualization (e.g., CartoDB and Zooniverse), data cleaning (e.g., VertNet, Encyclopedia of Life, Global Names, FilteredPush, Kurator, SALIX), and georeferencing (GeoLocate and CoGE).

Sophia_presentation

On Day 1, Austin Mast (Florida State Univ.) and Rob Guralnick (Univ. of Florida) welcomed everyone and provided brief introductions to iDigBio, Biospex, and Notes from Nature before lightning intros from each participant. Next, Libby Ellwood (Florida State Univ,), Austin, and Rob provided an introduction to proposed activities at the hackathon. These had been developed by iDigBio’s Interoperability for Public Participation in Digitization working group—the hackathon’s organizing committee (including those three plus Ed Gilbert, Nelson Rios, Ben Brumfield, Paul Flemons, and Greg Newman). These activities were presented as occurring in one of two tracks. The first track focused on innovative cross-platform ways to deploy and manage public participation projects, visualize and analyze progress for the project managers, and ingest data and provenance back into data management systems; this group would later be dubbed “Team Tardigrade.” The second track focused on development of novel ways to engage citizen scientists (e.g., via visualizations of individual and collective contributions); this would become “Team Honey Badger.” After this, Cody Meche gave an engaging talk on Agile development best practices and we split into our teams to develop priorities, goals for deliverables, and a road map.

What followed in Days 2 and 3 were a series of code-sprints interspersed with animated stand-ups, all fueled with a lot of coffee, hot tea, and food. In the end, each team went on to produce several deliverables involving subsets of their members that far exceeded expectations. Content regarding the deliverables can be found at the CITStitch wiki page. We have summarized the work briefly below. But as was emphasized at the start of the hackathon, successes will also be measured by the number of long-term collaborations initiated over dinner at the Reggae Shack, The Top or Andaz Indian Restaurant.

Listening_intently

Team Tardigrade

Stuart Lynn (Zooniverse) produced a broadly useful web service and data explorer for the (now 1 million!) transcriptions in Notes from Nature.
Ed Gilbert (Symbiota) and Daryl Lafferty (SALIX) produced a SALIX web service that will take an OCR text string and direct it to the correct SALIX-enabled Symbiota portal for processing; this SALIX-parsed data then can be sent to a transcription tool for proofreading.
John Wieczorek (UC–Berkeley), David Lowery (Harvard), and Dmitry Mozzherin (Marine Biological Lab, Woods Hole) produced web services for assessing the fitness for use of data and doing data cleaning, including validators for scientific name, year collected, collection locality coordinates, and measure of coordinate uncertainty.
Ben Brumfield (FromthePage.com), Greg Riccardi (Florida State Univ.), and Robert Bruhn (iDigBio’s Biospex) expanded the Biospex data model to include ledger and field book pages in anticipation of adding FromthePage as an actor in Biospex project workflows.
Finally, Greg Riccardi, Ed Gilbert, Nelson Rios (Tulane Univ.), Ben Brumfield, Robert Bruhn, and Austin Mast established a manifest file example in JSON that enables tools and project management systems to communicate about the public participation projects.

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Team Honey Badger

Chris Snyder (Zooniverse), with help from Libby Ellwood (Florida State Univ.) and Rob Guralnick (University of Florida), created functionality in Notes from Nature that compares entered taxonomic names against the GBIF Name API and gives feedback to inform the citizen scientist as to whether the name exists in GBIF and the number of records associated with that name; this gives the participant a sense of the significance of their contribution.
Julie Allen (Illinois Natural History Survey), Charlotte Germain (Univ. of Florida), Sophia B Liu (USGS iCoast) and Andrew Hill (CartoDB) created dynamic maps to visualize citizen science contributions; for example, the participant could upload a dataset to cartodb.com and select subsets of the data to display the country of origin for specimens that have been transcribed. Click here for a map of countries with specimens that have been digitized in Notes from Nature.
Paul Kimberly (Smithsonian), Paul Flemons (Australian Museum), Deb Paul (iDigBio), Libby, Rob, and Austin fleshed out a proposal for a 4-day global transcription blitz organized by the major transcription centers, including its timing, name, goals, funding, and organizational structure, and scoped the functionality for its website in years 1 and later (more to come on that in future blog posts!).
And, especially relevant to the global transcription blitz website, Alex Thompson (iDigBio) produced a prototype that integrates results across different transcription platforms and generates summary results and means for further exploration using Elasticsearch.

Thank you to all of our participants—what a great experience! You can check out more photos in the iDigBio CitStitch Hackathon album on facebook.

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