Update README.md (#11)

- Update README.md (dccab9ca16b568fb72dd992fe78fe150f09be642)


Co-authored-by: Sydne Record <[email protected]>

README.md

@@ -197,13 +197,12 @@ The full citation for the NEON ground beetle data for the closest release year t
 NEON (National Ecological Observatory Network). Ground beetles sampled from pitfall traps (DP1.10022.001), RELEASE-2021. https://doi.org/10.48443/tx5f-dy17. Dataset accessed from https://data.neonscience.org/data-products/DP1.10022.001/RELEASE-2021 on August 11, 2024.
 
 #### Who are the source data producers?
-[More Information Needed]
 <!-- This section describes the people or systems who originally created the data.
 
 Ex: This dataset is a collection of images taken of the butterfly collection housed at the Ohio State University Museum of Biological Diversity. The associated labels and metadata are the information provided with the collection from biologists that study butterflies and supplied the specimens to the museum.
  -->
 
-The beetles were preserved in ethanol following collection from NEON sites in 2018. They were were sent by [NEON](https://www.neonscience.org/) to Sydne Record and Isadora Fluck for imaging in 2022. Information regarding the sites from which they were collected and the taxonomic labels were provided by NEON. Site information (names and ecoclimatic domains) can be matched to `siteID` from the `NEON_Field_Site_Metadata_20240802.csv`, which is available on [NEON's field sites information page](https://www.neonscience.org/field-sites/explore-field-sites) (click `Download Field Site Table (CSV)`).
+This dataset is a collection of images taken from beetles collected by [NEON](https://www.neonscience.org/) field technicians that were preserved in ethanol following collection from NEON sites in 2018. A subset of difficult to ID taxa were pinned and sent to experts for identification. The images provided here were of more common species that did not require expert ID that could be identified by NEON field technicians. After being preserved in ethanol, the beetles were archived at the [NEON Biorepository] (https://biorepo.neonscience.org/portal/). They were were sent by Nico Franz, Kelsey Yule, and Andrew Johnston from the NEON Biorepository to Ben Baiser, Sydne Record, and Isadora Fluck for imaging in 2022. Information regarding the sites from which they were collected and the taxonomic labels were provided by NEON. Site information (names and ecoclimatic domains) can be matched to `siteID` from the `NEON_Field_Site_Metadata_20240802.csv`, which is available on [NEON's field sites information page](https://www.neonscience.org/field-sites/explore-field-sites) (click `Download Field Site Table (CSV)`).
 
 
 ### Annotations
@@ -212,20 +211,19 @@ If the dataset contains annotations which are not part of the initial data colle
 
 Ex: We standardized the taxonomic labels provided by the various data sources to conform to a uniform 7-rank Linnean structure. (Then, under annotation process, describe how this was done: Our sources used different names for the same kingdom (both _Animalia_ and _Metazoa_), so we chose one for all (_Animalia_). -->
 
-Annotations (elytra length and width) were completed in Zooniverse by Isadora Fluck and two summer REU students (Riley Wolcheski and Isha Chinniah); annotator is indicated by their NEON system usernames in the `BeetleMeasurements` CSV. The annotations (2 per beetle) were repeated for a subset of the images to measure observation error introduced in the annotation process. The taxonomic labels were provided by NEON with the samples.
+Annotations (elytra length and width) were completed in Zooniverse by Isadora Fluck and two Harvard Forest summer REU students (Riley Wolcheski and Isha Chinniah); annotator is indicated by their NEON system usernames in the `BeetleMeasurements` CSV. The annotations (2 per beetle) were repeated for a subset of the images to measure observation error introduced in the annotation process. The taxonomic labels were provided by NEON with the samples.
 
 #### Annotation process
-[More Information Needed: URL for Zooniverse?]
 <!-- This section describes the annotation process such as annotation tools used, the amount of data annotated, annotation guidelines provided to the annotators, interannotator statistics, annotation validation, etc. -->
 
-The images were downsized to 1MB (preserving aspect ratio) for annotation in Zooniverse. Overall, 234 images were annotated by all three annotators and 1 was annotated by just two. Beetles were indicated as not lying flat if they tended to one or the other side, as this can result in a smaller width measurement than expected. See the [sample image](https://huggingface.co/datasets/imageomics/BeetlePalooza/blob/main/beetles.png) (also in Figure 1) for indicators of length and width, as well as the centimeter mark in pixels on the scalebar.
+The images were downsized to 1MB (preserving aspect ratio) for annotation in [Zooniverse](https://www.zooniverse.org/). Overall, 234 images were annotated by all three annotators and 1 was annotated by just two. Beetles were indicated as not lying flat if they tended to one or the other side, as this can result in a smaller width measurement than expected. See the [sample image](https://huggingface.co/datasets/imageomics/BeetlePalooza/blob/main/beetles.png) (also in Figure 1) for indicators of length and width, as well as the centimeter mark in pixels on the scalebar.
 
 #### Who are the annotators?
 <!-- This section describes the people or systems who created the annotations. -->
 
-- Isadora E. Fluck: Ph.D. Candidate at Baiser Lab of Community Ecology University of Florida annotated all samples, and led annotation effort of two summer REU students:
-  - Riley Wolcheski
-  - Isha Chinniah
+- Isadora E. Fluck: Ph.D. Candidate at Baiser Lab of Community Ecology University of Florida annotated all samples, and led annotation effort of two summer REU students under the supervision of Sydne Record:
+  - Riley Wolcheski (University of Connecticut)
+  - Isha Chinniah (Mount Holyoke College)
 
 ### Personal and Sensitive Information
 <!-- 
@@ -240,13 +238,13 @@ Things to consider while working with the dataset. For instance, maybe there are
   - The `NEON_sampleID` RMNP_014.20180709.CALADV.01 is repeated because there were too many individuals in the sample to organize them all in one picture. Thus, the individuals from this sample are split between two pictures: `A00000051555_1` and `A00000051555_2`.
   - The `NEON_sampleID` MOAB_001.S.20180724 was provided without scientific name identification.
   - The `individual` indicator is not unique to `pictureID` since Zooniverse restarted IDs after individual number 99, so individuals are indicated by measurements annotated by `user_name == "IsaFluck"` since she annotated each image once, with the other annotators just labeling a subset for comparison.
-
+  - These images do not include all beetles sampled at all sites in 2018 because they do not include the pinned specimens.
+  - Dorsal images may not provide all the information needed to ID a beetle.
 
 ### Bias, Risks, and Limitations
-[More Information Needed]
 <!-- This section is meant to convey both technical and sociotechnical limitations. Could also address misuse, malicious use, and uses that the dataset will not work well for.-->
 
-This dataset does not have a balanced representation of genera.
+This dataset does not have a balanced representation of genera. In particular, rare or more difficult to ID taxa are not included here. These images do not include all beetles sampled at all sites in 2018 because they do not include the pinned specimens. 
 <!-- For instance, if your data exhibits a long-tailed distribution (and why). -->
 
 ### Recommendations