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
NOTE: This FAQ was updated in January 2018 and can be found here: https://blog.notesfromnature.org/2018/01/26/updated-faq-and-useful-tools-herbarium-interface-version-3/
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.
Success!
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!
The Valdosta State University Herbarium
Cabinets in the Valdosta State University Herbarium
The Valdosta State University Herbarium is a museum-quality collection preserving more than 65,000 dried plant specimens useful in research and teaching. The VSU Herbarium, a unit of the Biology Department of Valdosta State University and the second largest herbarium in Georgia, is a rich repository of data emphasizing the diverse flora of the coastal plain region of Georgia and, more generally, the flora of the southeastern United States. In addition to this geographic focus, the VSU Herbarium has taxonomic specialization beyond the southeastern region, with extensive holdings of sedges (Cyperaceae) and other graminoid families, and bryophytes (mosses).
Plant specimens in herbaria are the basis for the knowledge about where and when plants grow and their physical characteristics. Herbarium specimens and associated data are standards for the application of plant names and are widely used by scientists as a basis for the descriptions and distributional maps in specialized literature related to plants. Consequently, they are an essential resource for anyone who needs plant names consistently and accurately derived. The herbarium is also employed extensively to document the locations of rare species and how their populations change over time. Data from herbaria are now being used to study shifts in the timing of reproductive patterns (flowering and fruiting) of plants relating to climate change. Thus, herbarium specimens and data are useful to a variety of scientific researchers, not only botanists, but also ecologists, agricultural scientists and natural resource managers. The VSU Herbarium is used intensively in research and teaching at Valdosta State University, and it provides materials used by researchers at other institutions through lending and exchange of specimens.
Although it originated in the 1930s as a teaching resource of several hundred specimens collected by Professor Beatrice Nevins, the VSU Herbarium was founded as a research collection in 1967 by Professor Wayne R. Faircloth. In addition to Faircloth’s specimens, the VSU Herbarium includes significant collections of Charles Bryson, Richard Carter, Delzie Demaree, Robert Godfrey, Robert Kral, and Sidney McDaniel. Since 1984, the VSU herbarium has more than doubled in size, growing at the rate of 1000-2000 specimens per year. In 2001, the VSU Herbarium occupied new quarters with about 1500 sq. ft., more than twice the space of the old facility, and a modern dedicated climate control system with the capacity to maintain relative humidity below 60%. Additional information about the VSU Herbarium can be found here. Through support from the National Science Foundation, all of accessions in the VSU Herbarium have been imaged, and we are currently building a database of label data from these specimens. Through a local collaborative effort with the VSU Odum Library, many of these images are currently available on-line at http://herb.valdosta.edu.
The VSU Herbarium needs your help in building this database!
–Richard Carter, Director of the Valdosta State University Herbarium
Why do we need so many collections of the same plant?!
Figure from a paper by C. Lavoie and D. Lachance showing a shift toward earlier flowering time for coltsfoot (Tussilago farfara). Image used by permission of the Botanical Society of America.
When people first get a look inside of a herbarium cabinet they often ask: “why do you need so many specimens of the same plant species?” Well there are a few reasons for this. People who study plants don’t just want to see one example of a species. They may want to see multiple collections so that they can understand the variation in characters for the species. For example, the leaf shape may be highly variable so we would need to see different specimens to understand this. It may also be important to get an idea of all the places where a certain plant can be found. We would need several specimens from different locations to understand the geography. We may also want to know how characteristics of a plant, or its geographic distribution, might be changing over time. In this case, we would need collections from multiple years.
The change in when plants bloom (aka phenological shift) has received a lot of attention over the past few years. It is now well established that changes in the climate have caused many species to shift the timing of when the leaves emerge in the spring (leaf out) and when the flowers open. This shift has major implications. One example is that a plant might bloom before its pollinators are available. If pollination does not occur, this could result in the plant not being able to produce fruits and seeds, which are important for the future success of the species.
Herbarium specimens can be used in a relatively simple way to study phenological shifts.
American Hornbeam (Carpinus caroliniana) flowering in March 2007.
Using the date information provided on the specimen label, we can record the day of the year that different plant collections were made (e.g., collections showing flowers in bloom) and graph these values against the year. What is commonly found is that plants are blooming earlier as a response to a warmer climate. For example, the graphic at the right shows how a plant is blooming earlier. The collections made in the year 2000 bloomed several days earlier than the ones collected in 1920. The full article can be read here.
I am interested in knowing the date that plants were collected for a different reason.
For exotic species, or species that are relatively newly introduced into an area, it is valuable to know when they first arrived in a new place and how fast they are spreading. If we can locate the earliest museum records of a species in the United States for example, we can then trace its expansion to new areas over time using additional museum records (subsequent collections). We can then examine where the exotic species has spread and how fast. There are many factors that influence the spread of exotic species, but describing the basic aspects of their spread in space and time is a first important step in our efforts to understand this process.
The Notes From Nature projects asks citizen scientists to transcribe specimen labels in order to help record this kind of information that is important in ecological research. The date is a simple but extremely important piece of information. Phenological shifts and the spread of exotic species are two important issues that can be addressed using this information.
-Michael Denslow
What is an herbarium?
Researchers working in the herbarium at Appalachian State University
An herbarium is a place that houses plant specimens. Many people expect that an herbarium will be filled with living plants. However, these plant specimens are pressed, dried and glued to sheets of paper. They are dead. The sheets of paper are typically stored inside of cabinets for safekeeping and organizational purposes. An herbarium is similar to a library in that both house artifacts (specimens or books) in a safe and organized way that allows them to be found and used by researchers. If plant specimens are stored properly they will last hundreds of years with little sign of degradation.
If you think about it, it makes sense to store plant specimens in this way (as dead samples). Logistically you can fit and care for many more pressed specimens than living plants in the collection. In addition, an herbarium often contains plants from all over the world including plants from diverse habitats such as deserts and alpine tundra. It would be tough to grow all of these different plants in one place.
Herbaria are sometimes part of natural history museums, associated with botanic gardens or academic institutions. The largest herbarium collections in the world are housed in Paris and New York. These large collections contain millions of specimens. However most herbarium collections are much smaller. There are more than 3500 herbaria scattered across the world. In fact, you likely have a local herbarium that contains specimens of the plants that occur in your area. To learn more about the herbaria in your area you can search Index Herbariorum, a global directory of herbaria.
-Michael Denslow
Introduction to Notes From Nature
Michael Denslow collecting plants in central Tennessee, USA.
Humans have been collecting specimens from the natural world for centuries. These specimens include samples of rocks, minerals, plants, fungi and animals. In fact, a lot of the knowledge that we have about the earth’s plants and animals is based on specimens that were collected in nature. These specimens are now housed in natural history museums. The world’s great exploration expeditions often included teams of scientists that documented the things that they saw along the way. For example, Lewis and Clark’s expedition of the western United States resulted in the discovery of hundreds of plants and animals that were new to science.
Today, there are an estimated 2 billion specimens housed in natural history collections around the world. This incredible resource provides us with baseline information about the biodiversity of the earth. In addition, the data resulting from these specimens has been used to address a wide range of society’s pressing issues such as public health and environmental change.
However, for this resource to be used to it full potential there must be better digital access to the collections. Most natural history collections are housed in museum cabinets, where they are not easily available to citizens and researchers. It is estimated that only about 1/3 of all natural history specimens are available digitally over the Internet! In effect, the other 2/3 of this biodiversity information is locked away from view. This is despite the fact that the natural history museum community is committed to providing access to this data.
The Notes from Nature project is about digitally unlocking this treasure trove of biodiversity data. Contributions from the public or informally trained people have always played an important role in the field of natural history. These citizen scientists, as they are now called, have made many important contributions, including collecting specimens and even describe new species. Today’s technology provides us with new ways for people to engage with natural history collections, and to help promote access to this biodiversity resource.
The Notes from Nature project has built a tool that enables citizen scientists to make a scientifically relevant contribution though the transcription of specimen label information. Please consider helping us unlock this important information by taking some notes from nature. Every transcription that is completed brings us closer to the goal of providing access to this critical resource.
Take Notes From Nature!
Notes from Nature 