Modified data sources with urls and citations

README.md

@@ -89,20 +89,63 @@ English, Latin
 
 ### Source Data
 
-#### Data Collection and Processing
-
 We collected images of three taxonomic groups of organisms: fish, birds, and butterflies, each containing around 10k images. 
-Images for fish (Fish-10k) were curated from the larger image collection, FishAIR, which contains images from the Great Lakes Invasive Network Project (GLIN) and Integrated Digitized Biocollections (iDigBio). 
-These images originate from various museum collections such as INHS, FMNH, OSUM, JFBM, UMMZ and UWZM. We created the Fish-10k dataset by randomly sampling 10K images and preprocessing the images to crop and remove the background. For consistency, we leverage GroundingDINO to crop the fish body from the background and Segment Anything Model (SAM) to remove the background.
-We curated the images for butterflies (Butterfly-10k) from the Jiggins Heliconius Collection dataset, which has images collected from various sources. 
-We carefully sampled 10K images for Butterfly-10K from the entire collection to ensure the images capture unique specimens and represent a diverse set of species by adopting the following two steps. First, we filter out images with more than one image from the same view (i.e., dorsal or ventral).
-Second, we ensure each species has a minimum of 20 images and no more than 2,000 images. The images for birds (Bird-10k) are obtained from the CUB-200-2011 dataset by taking 190 species for which the common name to scientific name mapping is available. This results in a fairly balanced dataset with around 11K images in total.
+
+##### Fish
+
+Images for fish (Fish-10k) were curated from the larger image collection, [Fish-AIR](https://fishair.org/), which contains images from the [Great Lakes Invasives Network (GLIN)](https://greatlakesinvasives.org/portal/index.php) and [Integrated Digitized Biocollections (iDigBio)](https://www.idigbio.org/).
+
+These images originate from various museum collections, including the following:
+
+- [Illinois Natural History Survey (INHS)](https://biocoll.inhs.illinois.edu/portal/index.php)
+- [Minnesota Biodiversity Atlas, Bell Museum](https://bellatlas.umn.edu/index.php)
+- [University of Michigan Museum of Zoology (UMMZ), Division of Fishes](https://ipt.lsa.umich.edu/resource?r=ummz\_fish)
+- [University of Wisconsin-Madison Zoological Museum - Fish](http://zoology.wisc.edu/uwzm/)
+- [Field Museum of Natural History (Zoology, FMNH) Fish Collection](https://fmipt.fieldmuseum.org/ipt/resource?r=fmnh_fishes)
+- [The Ohio State University Fish Division, Museum of Biological Diversity (OSUM), Occurrence dataset](https://doi.org/10.15468/subsl8)
+
+[Phenoscape](https://kb.phenoscape.org/about/phenoscape/kb) and [FishBase](https://www.fishbase.se/search.php) were used to obtain the information on traits. 
+
+##### Bird
+
+We create the Bird-10k dataset from the [CUB-200-2011 dataset](https://www.vision.caltech.edu/datasets/cub_200_2011/). We obtain the scientific names from the [iNatLoc dataset](https://data.caltech.edu/records/ts54e-1jr46). 
+
+##### Butterflies
+
+We created the Butterfly-10k dataset from the [Heliconius Collection (Cambridege Butterfly) dataset](https://huggingface.co/datasets/imageomics/Heliconius-Collection_Cambridge-Butterfly).
+
+#### Data Processing
+
+##### Fish
+We created the Fish-10k dataset by randomly sampling 10K images and preprocessing the images to crop and remove the background. For consistency, we leverage [GroundingDINO](https://arxiv.org/abs/2303.05499) to crop the fish body from the background and [Segment Anything Model (SAM)](https://arxiv.org/abs/2304.02643) to remove the background.
+
+##### Bird
+
+For Bird-10k, we take 190 species for which the common name to scientific name mapping is available. This results in a fairly balanced dataset.
+
+##### Butterfly
+For the Butterfly-10k, we carefully sampled 10K images from the Heliconius Collection dataset to ensure the images capture unique specimens and represent a diverse set of species. We adopt the following steps:
+
+- We filter out images with more than one image from the same view (i.e., dorsal or ventral).
+- We ensure each species has a minimum of 20 images and no more than 2,000 images.
 
 ### Annotations
-The scientific names for the images of Fish-10k and Butterfly-10k were obtained directly from their respective sources. 
-For Bird-10k, we obtained the scientific names from the iNatLoc500 dataset. We curated around  31K question-answer pairs in both open and multiple-choice (MC) question-formats for evaluating species classification tasks. 
-The species-level trait presence/absence matrix for Fish-10k was manually curated with the help of biological experts co-authored in this paper. We leveraged the Phenoscape knowledge base with manual annotations to procure the presence-absence trait matrix.
-For Bird-10k, we obtained the trait matrix from the attribute annotations provided along with CUB-200-2011. We constructed approximately 380K question-answer pairs for trait identification tasks. 
+
+##### Scientific Names
+The scientific names for the images of **Fish-10k** and **Butterfly-10k** were obtained directly from their respective sources.
+
+For **Bird-10k**, we obtained the scientific names from the [iNatLoc dataset](https://data.caltech.edu/records/ts54e-1jr46). 
+
+In total, we curated around 31K question-answer pairs in both open and multiple-choice (MC) question-formats for evaluating species classification tasks. 
+
+##### Trait information
+The species-level trait presence/absence matrix for Fish-10k was manually curated with the help of biological experts co-authored in this paper. We leveraged the [Phenoscape knowledge base](https://kb.phenoscape.org/about/phenoscape/kb) and [FishBase](https://www.fishbase.se/search.php) along with manual annotations to procure the presence-absence trait information. We constructed approximately xK question-answer pairs for Fish-10k
+
+For Bird-10k, we obtained the trait matrix from the attribute annotations provided along with CUB-200-2011. 
+
+In total, we constructed approximately 380K question-answer pairs for trait identification tasks. 
+
+##### Grounding and referring
 For grounding and referring VQA tasks, the ground truths were manually annotated with the help of expert biologists on our team. We manually annotated bounding boxes corresponding to the traits of 500 fish specimens and 500 bird specimens, which are subsets of the larger Fish-10k and Bird-10k datasets, respectively. 
 We used the CVAT tool for annotation.
 
@@ -121,7 +164,7 @@ The data (images) contain a variety of licensing restrictions ranging from [CC0]
 
 
 ## Citation
-Please cite the following:
+Please cite our work as follows:
 
 ```
 @misc{maruf2024vlm4bio,
@@ -135,13 +178,24 @@ Please cite the following:
 }
 ```
 
+Please be sure to **also cite the original data sources** using all of the citations provided in the following:
+
+- Sources for Fish-10k: [metadata/fish-data-bib.bib](metadata/fish-data-bib.bib).
+- Sources for Bird-10k: [metadata/bird-data-bib.bib](metadata/bird-data-bib.bib)
+- Sources for Butterfly-10k: [metadata/butterfly-data-bib.bib](metadata/butterfly-data-bib.bib)
+
 ## Acknowledgements
 
 This work was supported by the Imageomics Institute, which is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under Award #2118240 (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
 
 
-## Dataset Card Authors 
+## Dataset Card Authors
+
+M. Maruf, Kazi Sajeed Mehrab and Elizabeth G. Campolongo
+
+## Dataset Card Contact
+
+marufm@vt.edu, ksmehrab@vt.edu
 
-M. Maruf (Contact mail: marufm@vt.edu)
 
 

metadata/bird-data-bib.bib

@@ -0,0 +1,16 @@
+@techreport{WahCUB_200_2011,
+	Title = ,
+	Author = {Wah, C. and Branson, S. and Welinder, P. and Perona, P. and Belongie, S.},
+	Year = {2011}
+	Institution = {California Institute of Technology},
+	Number = {CNS-TR-2011-001}
+}
+
+@inproceedings{cole2022label,
+  title={On label granularity and object localization},
+  author={Cole, Elijah and Wilber, Kimberly and Van Horn, Grant and Yang, Xuan and Fornoni, Marco and Perona, Pietro and Belongie, Serge and Howard, Andrew and Aodha, Oisin Mac},
+  booktitle={European Conference on Computer Vision},
+  pages={604--620},
+  year={2022},
+  organization={Springer}
+}

metadata/butterfly-data-bib.bib

@@ -0,0 +1,259 @@
+@misc{lawrence_campolongo_j2024,
+author = {Christopher Lawrence and Elizabeth G. Campolongo},
+title = {Heliconius Collection (Cambridge Butterfly)},
+year = 2024,
+publisher = {Hugging Face},
+url = {https://huggingface.co/datasets/imageomics/Heliconius-Collection_Cambridge-Butterfly}
+}
+
+@misc{but1_gabriela_montejo_kovacevich_2020_4289223,
+author = {Gabriela Montejo-Kovacevich and Eva van der Heijden and Nicola Nadeau and Chris Jiggins},
+title = {Cambridge butterfly wing collection batch 10},
+month = nov,
+year = 2020,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.4289223},
+url = {https://doi.org/10.5281/zenodo.4289223}
+}
+
+@misc{but2_patricio_a_salazar_2020_4288311,
+author = {Patricio A. Salazar and Nicola Nadeau and Gabriela Montejo-Kovacevich and Chris Jiggins},
+title = {{Sheffield butterfly wing collection - Patricio Salazar, Nicola Nadeau, Ikiam broods batch 1 and 2}},
+month = nov,
+year = 2020,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.4288311},
+url = {https://doi.org/10.5281/zenodo.4288311} 
+}
+
+@misc{but3_montejo_kovacevich_2019_2677821,
+author = {Montejo-Kovacevich, Gabriela and Jiggins, Chris and Warren, Ian},
+title = {Cambridge butterfly wing collection batch 2},
+month = may,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2677821},
+url = {https://doi.org/10.5281/zenodo.2677821} 
+}
+
+@misc{but4_jiggins_2019_2682458,
+author = {Jiggins, Chris and Montejo-Kovacevich, Gabriela and Warren, Ian and Wiltshire, Eva},
+title = {Cambridge butterfly wing collection batch 3},
+month = may,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2682458},
+url = {https://doi.org/10.5281/zenodo.2682458} 
+}
+
+@misc{but5_montejo_kovacevich_2019_2682669,
+author = {Montejo-Kovacevich, Gabriela and Jiggins, Chris and Warren, Ian},
+title = {Cambridge butterfly wing collection batch 4},
+month = may,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2682669},
+url = {https://doi.org/10.5281/zenodo.2682669} 
+}
+
+@misc{but6_montejo_kovacevich_2019_2684906,
+author = {Montejo-Kovacevich, Gabriela and Jiggins, Chris and Warren, Ian and Wiltshire, Eva},
+title = {Cambridge butterfly wing collection batch 5},
+month = may,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2684906},
+url = {https://doi.org/10.5281/zenodo.2684906} 
+}
+
+@misc{but7_warren_2019_2552371,
+author = {Warren, Ian and Jiggins, Chris},
+title = {{Miscellaneous Heliconius wing photographs (2001-2019) Part 1}},
+month = feb,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2552371},
+url = {https://doi.org/10.5281/zenodo.2552371} 
+}
+
+@misc{but8_warren_2019_2553977,
+author = {Warren, Ian and Jiggins, Chris},
+title = {{Miscellaneous Heliconius wing photographs (2001-2019) Part 3}},
+month = feb,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2553977},
+url = {https://doi.org/10.5281/zenodo.2553977} 
+}
+
+@misc{but9_montejo_kovacevich_2019_2686762,
+author = {Montejo-Kovacevich, Gabriela and Jiggins, Chris and Warren, Ian and Wiltshire, Eva},
+title = {Cambridge butterfly wing collection batch 6},
+month = may,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2686762},
+url = {https://doi.org/10.5281/zenodo.2686762} 
+}
+
+@misc{but10_jiggins_2019_2549524,
+author = {Jiggins, Chris and Warren, Ian},
+title = {{Cambridge butterfly wing collection - Chris Jiggins 2001/2 broods batch 1}},
+month = jan,
+year = 2019,
+publisher = {Zenodo},
+version = 1,
+doi = {10.5281/zenodo.2549524},
+url = {https://doi.org/10.5281/zenodo.2549524}
+}
+
+@misc{but11_jiggins_2019_2550097,
+author = {Jiggins, Chris and Warren, Ian},
+title = {{Cambridge butterfly wing collection - Chris Jiggins 2001/2 broods batch 2}},
+month = jan,
+year = 2019,
+publisher = {Zenodo},
+version = 1,
+doi = {10.5281/zenodo.2550097},
+url = {https://doi.org/10.5281/zenodo.2550097}
+}
+
+@misc{but12_joana_i_meier_2020_4153502,
+author = {Joana I. Meier and Patricio Salazar and Gabriela Montejo-Kovacevich and Ian Warren and Chris Jggins},
+title = {{Cambridge butterfly wing collection - Patricio Salazar PhD wild specimens batch 3}},
+month = oct,
+year = 2020,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.4153502},
+url = {https://doi.org/10.5281/zenodo.4153502}
+}
+
+@misc{but13_montejo_kovacevich_2019_3082688,
+author = {Montejo-Kovacevich, Gabriela and Jiggins, Chris and Warren, Ian},
+title = {{Cambridge butterfly wing collection batch 1- version 2}},
+month = may,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.3082688},
+url = {https://doi.org/10.5281/zenodo.3082688} 
+}
+
+@misc{but14_montejo_kovacevich_2019_2813153,
+author = {Montejo-Kovacevich, Gabriela and Jiggins, Chris and Warren, Ian and Salazar, Camilo and Elias, Marianne and Gavins, Imogen and Wiltshire, Eva and Montgomery, Stephen and McMillan, Owen},
+title = {{Cambridge and collaborators butterfly wing collection batch 10}},
+month = may,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2813153},
+url = {https://doi.org/10.5281/zenodo.2813153} 
+}
+
+@misc{but15_salazar_2018_1748277,
+author = {Salazar, Patricio and Montejo-Kovacevich, Gabriela and Warren, Ian and Jiggins, Chris},
+title = {{Cambridge butterfly wing collection - Patricio Salazar PhD wild and bred specimens batch 1}},
+month = dec,
+year = 2018,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.1748277},
+url = {https://doi.org/10.5281/zenodo.1748277} 
+}
+
+@misc{but16_montejo_kovacevich_2019_2702457,
+author = {Montejo-Kovacevich, Gabriela and Jiggins, Chris and Warren, Ian and Wiltshire, Eva},
+title = {Cambridge butterfly wing collection batch 7},
+month = may,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2702457},
+url = {https://doi.org/10.5281/zenodo.2702457}
+}
+
+@misc{but17_salazar_2019_2548678,
+author = {Salazar, Patricio and Montejo-Kovacevich, Gabriela and Warren, Ian and Jiggins, Chris},
+title = {{Cambridge butterfly wing collection - Patricio Salazar PhD wild and bred specimens batch 2}},
+month = jan,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2548678},
+url = {https://doi.org/10.5281/zenodo.2548678}
+}
+
+@misc{but18_pinheiro_de_castro_2022_5561246,
+author = {Pinheiro de Castro, Erika and Jiggins, Christopher and Lucas da Silva-Brand\u00e3o, Karina and Victor Lucci Freitas, Andre and Zikan Cardoso, Marcio and Van Der Heijden, Eva and Meier, Joana and Warren, Ian},
+title = {{Brazilian Butterflies Collected December 2020 to January 2021}},
+month = feb,
+year = 2022,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.5561246},
+url = {https://doi.org/10.5281/zenodo.5561246}
+}
+
+@misc{but19_montejo_kovacevich_2019_2707828,
+author = {Montejo-Kovacevich, Gabriela and Jiggins, Chris and Warren, Ian and Wiltshire, Eva},
+title = {Cambridge butterfly wing collection batch 8},
+month = may,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2707828},
+url = {https://doi.org/10.5281/zenodo.2707828}
+}
+
+@misc{but20_montejo_kovacevich_2019_2714333,
+author = {Montejo-Kovacevich, Gabriela and Jiggins, Chris and Warren, Ian and Wiltshire, Eva and Gavins, Imogen},
+title = {Cambridge butterfly wing collection batch 9},
+month = may,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2714333},
+url = {https://doi.org/10.5281/zenodo.2714333} 
+}
+
+@misc{but21_gabriela_montejo_kovacevich_2020_4291095,
+author = {Gabriela Montejo-Kovacevich and Eva van der Heijden and Chris Jiggins},
+title = {{Cambridge butterfly collection - GMK Broods Ikiam 2018}},
+month = nov,
+year = 2020,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.4291095},
+url = {https://doi.org/10.5281/zenodo.4291095}
+}
+
+@misc{but22_montejo_kovacevich_2021_5526257,
+author = {Montejo-Kovacevich, Gabriela and Paynter, Quentin and Ghane, Amin},
+title = {{Heliconius erato cyrbia, Cook Islands (New Zealand) 2016, 2019, 2021}},
+month = sep,
+year = 2021,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.5526257},
+url = {https://doi.org/10.5281/zenodo.5526257}
+}
+
+@misc{but23_warren_2019_2553501,
+author = {Warren, Ian and Jiggins, Chris},
+title = {{Miscellaneous Heliconius wing photographs (2001-2019) Part 2}},
+month = feb,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2553501},
+url = {https://doi.org/10.5281/zenodo.2553501} 
+}
+
+@misc{but24_salazar_2019_2735056,
+author = {Salazar, Camilo and Montejo-Kovacevich, Gabriela and Jiggins, Chris and Warren, Ian and Gavins, Imogen},
+title = {{Camilo Salazar and Cambridge butterfly wing collection batch 1}},
+month = may,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2735056},
+url = {https://doi.org/10.5281/zenodo.2735056} 
+}
+
+@misc{but25_mattila_2019_2555086,
+author = {Mattila, Anniina and Jiggins, Chris and Warren, Ian},
+title = {{University of Helsinki butterfly collection - Anniina Mattila bred specimens}},
+month = feb,
+year = 2019,
+publisher = {Zenodo},
+doi = {10.5281/zenodo.2555086},
+url = {https://doi.org/10.5281/zenodo.2555086} 
+}

metadata/fish-data-bib.bib

@@ -0,0 +1,92 @@
+@dataset{inhs,
+    title ={INHS collections data} ,
+    journal ={http://biocoll.inhs.illinois.edu/portal/index.php} ,
+    year ={2022} 
+}
+
+@article{jfbm,
+    title ={JFBM Bell Atlas} ,
+    journal = {http://bellatlas.umn.edu/index.php} ,
+    year = 2022
+}
+
+@article{ummz,
+    title ={UMMZ University of Michigan Museum of Zoology, Division of Fishes},
+    journal = {https://ipt.lsa.umich.edu/resource?r=ummz\_fish}
+}
+
+@article{umadison,
+    title ={University of Wisconsin-Madison Zoological Museum - Fish} ,
+    journal ={http://zoology.wisc.edu/uwzm/}
+}
+
+@article{fmnh,
+    title ={FMNH Field Museum of Natural History (Zoology) Fish Collection} ,
+    journal ={Field Museum. https://fmipt.fieldmuseum.org/ipt/resource?r=fmnh_fishes}
+}
+
+@article{osum,
+    author ={Daly M, Johnson N} ,
+    title ={Ohio State University Fish Division (OSUM)} ,
+    journal ={Museum of Biological Diversity, The Ohio State University. Occurrence dataset, https://doi.org/10.15468/subsl8},
+    year = 2018
+}
+
+@article{fishair,
+    title ={Multimedia of Fish Specimen and associated metadata. Fish-AIR},
+    journal ={Biology guided Neural Network. Tulane University Biodiversity Research Institute (https://fishair.org).}
+}
+
+@article{Morphbank,
+    title ={Morphbank: Biological Imaging (https://www.morphbank.net/)} ,
+    journal ={Florida State University, Department of Scientific Computing, Tallahassee, FL 32306-4026 USA.}
+}
+@article{glin,
+    title ={Great Lakes Invasives Network Project},
+journal = {https://greatlakesinvasives.org/portal/index.php}
+}
+
+@article{IDigBio,
+    title ={iDigBio } ,
+    journal ={http://www.idigbio.org/portal},
+    year = {2020}
+}
+
+@incollection{mabee2018phenoscape,
+  title={Phenoscape: semantic analysis of organismal traits and genes yields insights in evolutionary biology},
+  author={Mabee, Paula M and Dahdul, Wasila M and Balhoff, James P and Lapp, Hilmar and Manda, Prashanti and Uyeda, Josef and Vision, Todd and Westerfield, Monte},
+  booktitle={Application of Semantic Technology in Biodiversity Science},
+  pages={207--224},
+  year={2018},
+  publisher={IOS Press}
+}
+
+@online{fishbase,
+  author       = {Froese, R. and Pauly, D.},
+  title        = {FishBase},
+  year         = {2024},
+  note         = {World Wide Web electronic publication. Version 02/2024},
+  url          = {http://www.fishbase.org}
+}
+
+@article{edmunds2015phenoscape,
+  title={Phenoscape: identifying candidate genes for evolutionary phenotypes},
+  author={Edmunds, Richard C and Su, Baofeng and Balhoff, James P and Eames, B Frank and Dahdul, Wasila M and Lapp, Hilmar and Lundberg, John G and Vision, Todd J and Dunham, Rex A and Mabee, Paula M and others},
+  journal={Molecular Biology and Evolution},
+  volume={33},
+  number={1},
+  pages={13--24},
+  year={2015},
+  publisher={Society for Molecular Biology and Evolution}
+}
+
+@article{mabee2012500,
+  title={500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton},
+  author={Mabee, Paula and Balhoff, James P and Dahdul, Wasila M and Lapp, Hilmar and Midford, Peter E and Vision, Todd J and Westerfield, Monte},
+  journal={Journal of Applied Ichthyology},
+  volume={28},
+  number={3},
+  pages={300--305},
+  year={2012},
+  publisher={Wiley Online Library}
+}