Add annotation descriptions from Wasila
Browse files
README.md
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@@ -171,7 +171,7 @@ CSV Columns are as follows:
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- `adipose_fin`: Presence/absence of the adipose fin trait. NA for the classification (FV-419) dataset, since it is only used for identification. 1 indicates presence and 0 indicates absence. This is used for trait identification.
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- `pelvic_fin`: Presence/absence of the pelvic trait. NA for the classification (FV-419) dataset, since it is only used for identification. 1 indicates presence and 0 indicates absence. This is only used for trait identification.
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- `barbel`: Presence/absence of the barbel trait. NA for the classification (FV-419) dataset, since it is only used for identification. 1 indicates presence and 0 indicates absence. This is used for trait identification.
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- `multiple_dorsal_fin`: Presence/absence of the
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**Note:**
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@@ -193,14 +193,16 @@ The ultimate goal of Fish-Vista is to provide a clean, carefully curated, high-r
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### Source Data
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<!-- This section describes the source data (e.g., news text and headlines, social media posts, translated sentences, ...). As well as an original source it was created from (e.g., sampling from Zenodo records, compiling images from different aggregators, etc.) -->
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Images and taxonomic labels were aggregated by [Fish-AIR](https://fishair.org/) from
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[Phenoscape](https://kb.phenoscape.org/about/phenoscape/kb) and [FishBase](https://www.fishbase.se/search.php) were used to standardize the species labels and provided the information on expected traits at the species level.
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[Phenoscape](https://kb.phenoscape.org/about/phenoscape/kb) and [FishBase](https://www.fishbase.se/search.php) were used to standardize the species labels provided by Fish-AIR. They also provided the information on expected species-level traits.
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Image-level traits were manually annotated as described below.
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### Personal and Sensitive Information
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- `adipose_fin`: Presence/absence of the adipose fin trait. NA for the classification (FV-419) dataset, since it is only used for identification. 1 indicates presence and 0 indicates absence. This is used for trait identification.
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- `pelvic_fin`: Presence/absence of the pelvic trait. NA for the classification (FV-419) dataset, since it is only used for identification. 1 indicates presence and 0 indicates absence. This is only used for trait identification.
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- `barbel`: Presence/absence of the barbel trait. NA for the classification (FV-419) dataset, since it is only used for identification. 1 indicates presence and 0 indicates absence. This is used for trait identification.
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- `multiple_dorsal_fin`: Presence/absence of the dorsal fin trait. NA for the classification (FV-419) dataset, since it is only used for identification. 1 indicates presence, 0 indicates absence and -1 indicates unknown. This is used for trait identification.
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**Note:**
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### Source Data
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<!-- This section describes the source data (e.g., news text and headlines, social media posts, translated sentences, ...). As well as an original source it was created from (e.g., sampling from Zenodo records, compiling images from different aggregators, etc.) -->
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Images and taxonomic labels were aggregated by [Fish-AIR](https://fishair.org/) from
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- [Great Lakes Invasives Network (GLIN)](https://greatlakesinvasives.org/portal/index.php)
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- [iDigBio](https://www.idigbio.org/)
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- [Morphbank](https://www.morphbank.net/)
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- [Illinois Natural History Survey (INHS)](https://biocoll.inhs.illinois.edu/portal/index.php)
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- [Minnesota Biodiversity Atlas, Bell Museum](https://bellatlas.umn.edu/index.php)
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- [University of Michigan Museum of Zoology (UMMZ), Division of Fishes](https://ipt.lsa.umich.edu/resource?r=ummz\_fish)
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- [University of Wisconsin-Madison Zoological Museum - Fish](http://zoology.wisc.edu/uwzm/)
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- [Field Museum of Natural History (Zoology, FMNH) Fish Collection](https://fmipt.fieldmuseum.org/ipt/resource?r=fmnh_fishes)
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- [The Ohio State University Fish Division, Museum of Biological Diversity (OSUM), Occurrence dataset](https://doi.org/10.15468/subsl8)
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[Phenoscape](https://kb.phenoscape.org/about/phenoscape/kb) and [FishBase](https://www.fishbase.se/search.php) were used to standardize the species labels and provided the information on expected traits at the species level.
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[Phenoscape](https://kb.phenoscape.org/about/phenoscape/kb) and [FishBase](https://www.fishbase.se/search.php) were used to standardize the species labels provided by Fish-AIR. They also provided the information on expected species-level traits.
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Image-level traits were manually annotated as described below.
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The annotation process for the segmentation subset was led by Wasila Dahdul. She provided guidance and oversight to a team of three people from [NEON](https://www.neonscience.org/about), who used [CVAT](https://zenodo.org/records/7863887) to label nine external traits in the images. These traits correspond to the following terms for anatomical structures in the UBERON anatomy ontology:
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1. Eye, [UBERON_0000019](http://purl.obolibrary.org/obo/UBERON_0000019)
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2. Head, [UBERON_0000033](http://purl.obolibrary.org/obo/UBERON_0000033)
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3. Barbel, [UBERON_2000622](http://purl.obolibrary.org/obo/UBERON_2000622)
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4. Dorsal fin, [UBERON_0003097](http://purl.obolibrary.org/obo/UBERON_0003097)
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5. Adipose fin, [UBERON_2000251](http://purl.obolibrary.org/obo/UBERON_2000251)
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6. Pectoral fin, [UBERON_0000151](http://purl.obolibrary.org/obo/UBERON_0000151)
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7. Pelvic fin, [UBERON_0000152](http://purl.obolibrary.org/obo/UBERON_0000152)
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8. Anal fin, [UBERON_4000163](http://purl.obolibrary.org/obo/UBERON_4000163)
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9. Caudal fin, [UBERON_4000164](http://purl.obolibrary.org/obo/UBERON_4000164)
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### Personal and Sensitive Information
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