update labels (species just species epithet) (#8)

- update labels (species just species epithet) (7a516055bb65bee4f753bfaf6fb3c8c6a8707d5c)
- Fix taxonomic data in catalog and embeddings; add image URLs (a98ee3426c62535d227af8bd8b8c374686965dbf)
- Apply UTF-8 encoding (fecee2056014861942542abb1744a31047f1c572)
- Update column descriptions to match revised catalog (a849013fd04d1ceb524ab568257bb39b4fd36e86)


Co-authored-by: Matthew Thompson <[email protected]>

README.md

@@ -126,21 +126,22 @@ Each image in this dataset is matched to the [7-rank Linnean taxonomy](https://w
 
 **catalog.parquet**
  - `uuid`: unique identifier for the image in this dataset, created at time of download.
+ - `source_url`: URL from which the image was downloaded, used to preview image in viewer.
  - `kingdom`: kingdom to which the subject of the image belongs (`Animalia`, `Plantae`, `Fungi`, `Chromista`, `Protozoa`, `Bacteria`, `Viruses`, `Archaea`, and less than 1% unresolved cases, e.g., `Metazoa` and `incertae sedis`).
  - `phylum`: phylum to which the subject of the image belongs.
  - `class`: class to which the subject of the image belongs.
  - `order`: order to which the subject of the image belongs.
  - `family`: family to which the subject of the image belongs.
  - `genus`: genus to which the subject of the image belongs.
- - `species`: species to which the subject of the image belongs.
+ - `species`: species to which the subject of the image belongs; note that this is the specific epithet.
  - `scientific_name`: `<Genus> <species>`  of the subject of the image, or most specific taxonomic rank available.
- - `common`: vernacular name associated with the subject of the image where available. Otherwise, this is either the `scientific_name` or whatever subset of the taxonomic hierarchy is available (eg., `<Kingdom> <Phylum> <Class> <Order>` or `<Kingdom> <Phylum> <Class> <Order> <Family>`). All images have a non-null entry for this column.
- - `source_id`: unique identifier for the image used by the source. 
-    - **Note:** for GBIF, this is `gbifID` which is unique to the _occurrence_ containing the image. For EOL, this is `<EOL Content ID>_<EOL Page ID>`, the first of which is not a persistent identifier.
+ - `common`: vernacular name associated with the subject of the image where available. Common name is sourced from GBIF vernacular names provided in the [GBIF Backbone Taxonomy](https://doi.org/10.15468/39omei).
  - `data_source`: source from which the record was obtained (`gbif`, `eol`, `bioscan`, or `fathomnet`).
  - `publisher`: the organization or entity that published the data (exclusive to GBIF records).
  - `basisOfRecord`: basis of the record (e.g., `PRESERVED_SPECIMEN`, `HUMAN_OBSERVATION`, `MACHINE_OBSERVATION`; exclusive to GBIF records).
- - `img_type`: the type of the associated image or its subject (e.g., `Museum Specimen: Fungi`, `Citizen Science`, `Camera-trap`), as defined by our processing (exclusive to GBIF records; EOL, BIOSCAN, and FathomNet images are all classified as `Unidentified). 
+ - `img_type`: the type of the associated image or its subject (e.g., `Museum Specimen: Fungi`, `Citizen Science`, `Camera-trap`), as defined by our processing (exclusive to GBIF records; EOL, BIOSCAN, and FathomNet images are all classified as `Unidentified).
+ - `source_id`: unique identifier for the image used by the source.
+    - **Note:** for GBIF, this is `gbifID` which is unique to the _occurrence_ containing the image. For EOL, this is `<EOL Content ID>_<EOL Page ID>`, the first of which is not a persistent identifier.
  - `shard_filename`: name of shard containing the image.
  - `shard_file_path`: filepath of the shard containing the image.
 	- ex: `200M_v1.1/224x224/shards/shard-00123.tar`

dataset/catalog.parquet

@@ -1,3 +1,3 @@
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-oid sha256:a0b370c285bf95c939a60a3ea70e4ce2f2f2b5ad076670cca83d32868fd5f748
-size 12594559780
+oid sha256:39abfb7db1fc4bcb09f08618e205586f7e3fee6ca9f3589008e964d594523cd2
+size 13876288366

embeddings/txt_emb_species.json

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:da79f083fbfe6f668d4a9b38403e6ed8c0d06af7150e560ed5607bb66f86caa0
-size 169045004
+oid sha256:0888c4a19c84d83b4b87a9ea26ce02cacce7341062d24b2c2060867dcde8f999
+size 172416395