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 (https://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.

https://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.

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