DOI: 10.5281/zenodo.5711874
title: Global Biotic Interactions: Elton Dataset Cache

description: Global Biotic Interactions: Elton Dataset Cache The intended use of this archive/cache is to allow for offline-enabled access versions of existing species interaction datasets. The program "Elton" (https://doi.org/10.5281/zenodo.998263) was used to populate the content of elton-datasets.tar.gz . The same program can be used to extract information from the cache archive also. Global Biotic Interactions (https://globalbioticinteractions.org, https://doi.org/10.1016/j.ecoinf.2014.08.005) also uses these archives to create derived species interaction data archives, search indexes and APIs. Please note that due to size considerations, offline-enabled access to an elton dataset cache of iNaturalist interaction data has been excluded from this publications and moved into a separate Zenodo publication at https://doi.org/10.5281/zenodo.3950546 . Contents<br> -------- README:<br> this file elton-datasets.tar.gz:<br> versioned archive with species interaction datasets elton-datasets.tar.sha256:<br> content signature of elton-datasets.tar elton-datasets.tsv:<br> list of included datasets elton.jar:<br> commandline program to help access the species interaction datasets Usage<br> ----- To install, extract elton-datasets.tar.gz into a directory of choice using: tar xfz elton-dataset.tar.gz To use, download elton.jar included this publication and execute the following to get a list of available datasets: java -Xmx4G -jar elton.jar datasets on a system that has java v8+ installed. If all goes well, you should be able to regenerate the included file elton-dataset.tsv . For more information on how to use elton.jar, execute: java -jar elton.jar usage or visit https://github.com/globalbioticinteractions/elton for more available commands. Alternatively, without using Elton, you can access the data by inspecting the access.tsv files in the various directories of the datasets directory. When using these datasets in a publication or product, please cite the *original* data providers and publications. You can find the citations in the data. Included datasets: AgentschapPlantentuinMeise/ashForestInteractions Groom, Q.J., Maarten De Groot, M. & Marčiulynienė, D. (2020) Species interation data manually extracted from literature for species . https://github.com/AgentschapPlantentuinMeise/ashForestInteractions/archive/0a73fdc7a424a52ec8398cd153e9fb8b5f465eb2.zip 2021-11-12T23:10:59.455Z fa9cc04c03589a97e2047d534f3e7ba9c8f02805e92d396c1b640b3344a110be 0.12.2<br> BDMYRepository/Echino-Interactions Soleto-Casas RC and Simões N (2020). Parasitic and commensal invertebrates of echinoderms from American Tropical And Subtropical Atlantic manually extracted from literature. https://zenodo.org/record/3742346/files/BDMYRepository/Echino-Interactions-V3.zip 2021-11-12T23:11:17.748Z 888e5165881b5d3533fc1502300f21d3421abf0af6ccc2bc06b2c90f6b9a58f7 0.12.2<br> BDMYRepository/Paguroidea-Mollusca-Interactions Cervantes-Campero G and Simões N (2020). Use of shells (Mollusca) by hermit crabs (Paguroidea) from the Southern Gulf of Mexico and the Caribbean Sea. https://zenodo.org/record/3901657/files/BDMYRepository/Paguroidea-Mollusca-Interactions-1.1.zip 2021-11-12T23:11:25.778Z d35f79522c66505bcd1b676c9c39c70725f195b64434568f90b0ef2d82956e56 0.12.2<br> BDMYRepository/Sponge_Interactions Pérez-Botello A M and Simões N (2019). Sponge-dwelling fauna from the Gulf of Mexico and the Caribbean sea a manually extracted from literature. V2.0 https://zenodo.org/record/4544355/files/BDMYRepository/Sponge_Interactions-2.06.zip 2021-11-12T23:11:34.611Z 29b599e9cc46659381c45365dc9dc5d8e2f2490f6eb379ace41b7ada667c9f53 0.12.2<br> Big-Bee-Network/bee-interaction-database Seltmann, K., Van Wagner, J., Behm, R., Brown, Z., Tan, E., & Liu, K. (2020). BID: A project to share biotic interaction and ecological trait data about bees (Hymenoptera: Anthophila). UC Santa Barbara: Cheadle Center for Biodiversity and Ecological Restoration. Retrieved from https://escholarship.org/uc/item/1g21k7bf https://github.com/Big-Bee-Network/bee-interaction-database/archive/99659e611eaf6594d11f913d18eabae51ff09bef.zip 2021-11-12T23:11:56.872Z 02873ad486861456acddd80ac444cc7e8828b7eae1985ca11e5c8cbb26ce966e 0.12.2<br> CALeDNA/Klamath-mountains Genus level interactions from a metagenomic analysis of eDNA samples from the Klamath mountains https://github.com/CALeDNA/Klamath-mountains/archive/2a885acccb9c7d8f0f368044d9ba71d74c309450.zip 2021-11-12T23:12:03.156Z 8bdedeb77ef6ec5be27937768adaf20d48671be636bffb79eb9d278d8bb666ed 0.12.2<br> EMTuckerLabUMMZ/ummzi University of Michigan Museum of Zoology Insect Division. Full Database Export 2020-11-20 provided by Erika Tucker and Barry Oconner. https://github.com/EMTuckerLabUMMZ/ummzi/archive/6731357a377e9c2748fc931faa2ff3dc0ce3ea7a.zip 2021-11-12T23:12:53.239Z 2c8c0ec09c6b0509882ad2d98a8a1ee1d1ea870c3ab2e7d69a0486f2e4643b01 0.12.2<br> EOL/pseudonitzchia A. Thessen. 2014. Species associations extracted from EOL text data objects via text mining. https://github.com/EOL/pseudonitzchia/archive/e5838965a186fba4b7215cd0d179c4526773bad5.zip 2021-11-12T23:14:06.961Z c68c9950743e245a54937e84a725ea945f272eb271392b762a2da00577e44db8 0.12.2<br> Extended-Bee-Network/bee-interaction-database Seltmann, K., Van Wagner, J., Behm, R., Brown, Z., Tan, E., & Liu, K. (2020). BID: A project to share biotic interaction and ecological trait data about bees (Hymenoptera: Anthophila). UC Santa Barbara: Cheadle Center for Biodiversity and Ecological Restoration. Retrieved from https://escholarship.org/uc/item/1g21k7bf https://github.com/Extended-Bee-Network/bee-interaction-database/archive/99659e611eaf6594d11f913d18eabae51ff09bef.zip 2021-11-12T23:14:18.705Z 02873ad486861456acddd80ac444cc7e8828b7eae1985ca11e5c8cbb26ce966e 0.12.2<br> Faizaufa/redhead2018 Redhead, J.W.; Coombes, C.F.; Dean, H.J.; Dyer, R.; Oliver, T.H.; Pocock, M.J.O.; Rorke, S.L.; Vanbergen, A.J.; Woodcock, B.A.; Pywell, R.F. (2018). Plant-pollinator interactions database for construction of potential networks. NERC Environmental Information Data Centre. https://doi.org/10.5285/6d8d5cb5-bd54-4da7-903a-15bd4bbd531b https://github.com/Faizaufa/redhead2018/archive/89ca7296078cce01a293813e509700d6c05faabc.zip 2021-11-12T23:14:23.735Z 1c7ea5a4d2cf7d51718723adaa2e36e0d936518921b7db8c02988cc37cacaa5c 0.12.2<br> FloraVincent/DIDB Flora Vincent. 2019. DIDB: Diatom Interaction DataBase. https://github.com/FloraVincent/DIDB/archive/c5146d235b6d0701d8828d518bb7f290a5633a31.zip 2021-11-12T23:14:40.111Z 045e44bc71c26b826a30932236254fac4727fce6b9a1a77cd3422ba28e8fe7a0 0.12.2<br> GoMexSI/JLewis_GoMexSi http://gomexsi.tamucc.edu https://github.com/GoMexSI/JLewis_GoMexSi/archive/f55ee847661a28b136a86f6669e81669f656fc1b.zip 2021-11-13T04:21:02.172Z 01d7c985a183f74a69a709e342252489417fb667a28c66c461bc71043835a0bc 0.12.2<br> GoMexSI/abascal http://gomexsi.tamucc.edu https://github.com/GoMexSI/abascal/archive/d2bbfcdfa4499ecc7fb021cee66aae05139b9a08.zip 2021-11-13T04:20:12.703Z 4486a9ea58c7401723df75dafc2b5f24ce275d7e7edf5defb56bc5cc1103a9fc 0.12.2<br> GoMexSI/akin Akin, S., & Winemiller, K. O. (2006). Seasonal variation in food web composition and structure in a temperate tidal estuary. Estuaries and Coasts, 29(4), 552–567. doi:10.1007/bf02784282 https://github.com/GoMexSI/akin/archive/6fc86470c20812be325612f51783ae3e7342a2ea.zip 2021-11-13T04:20:27.551Z da0b6f7eb2436d7123c24ddf44d49c388b44d770604558d54943968e834fce03 0.12.2<br> GoMexSI/baremore Baremore, I., Murie, D., & Carlson, J. (2010). Seasonal and size-related differences in diet of the Atlantic angel shark Squatina dumeril in the northeastern Gulf of Mexico. Aquatic Biology, 8, 125–136. doi:10.3354/ab00214 https://github.com/GoMexSI/baremore/archive/de843f7a86b9cb2e5b2d511e9082e13c7b88862f.zip 2021-11-13T04:20:31.971Z ed5b533a989052437aeee0ad2096ff3d22cca734ecbf720e23bd2e7b4327ecff 0.12.2<br> GoMexSI/blewett Blewett, D. A., Hensley, R. A., & Stevens, P. W. (2006). Feeding Habits of Common Snook, Centropomus undecimalis, in Charlotte Harbor, Florida. Gulf and Caribbean Research, 18. doi:10.18785/gcr.1801.01 https://github.com/GoMexSI/blewett/archive/922e3ed1531d2af5720fdbc0307a1942b5ac050d.zip 2021-11-13T04:20:36.806Z 0bf13b222406591c19c4b8305e2a1e9416765ab94c8d729fe4213e814c0542b6 0.12.2<br> GoMexSI/interaction-data http://gomexsi.tamucc.edu https://github.com/GoMexSI/interaction-data/archive/05dcb4f75951950dead51d6f693ba24a87db9a92.zip 2021-11-13T04:20:46.610Z ed9062d4bb06ce6136f367b0c2180b4502ecee88fe8acdcbc6b145a3812824de 0.12.2<br> GoMexSI/simons Simons JD. 1997. Food habits and trophic structure of the demersal fish assemblages on the Mississippi-Alabama continental shelf. PhD Thesis. https://github.com/GoMexSI/simons/archive/5af33796c194bed634bffc3790ed540d42fa03aa.zip 2021-11-13T04:21:16.191Z 6cfad1260fdf4d6fc0d3776f15b3c5e9053b960da74a8f3367a76a05c892c6ec 0.12.2<br> GoMexSI/wrast Wrast JL. 2008. Spatiotemporal And Habitat-mediated Food Web Dynamics in Lavaca Bay, Texas. Master Thesis. https://github.com/GoMexSI/wrast/archive/6a06057d7f3ccc4204378573ca03725862256d0c.zip 2021-11-13T04:21:21.312Z 30e9f0533a5c1a15c291bbb64d5e5fc3f77ea7fb4ebf7b07fc0ea9abef2ffa20 0.12.2<br> KatjaSchulz/dinosaur-biotic-interactions Katja Schulz. 2015. Information about dinosaur diets manually extracted from literature. https://github.com/KatjaSchulz/dinosaur-biotic-interactions/archive/e744bef6ff47d57b86b81fe767ad983ef5b7f460.zip 2021-11-13T04:24:36.498Z 39c57bf7c59637e4495e68746743421f6e07fa61d9d25495fd92210be1333324 0.12.2<br> NASUA/ZalophusPredatoryInteractions Carranco.S ; Muñoz, G. 2018. Galapagos sea lion fish-feeding interaction dataset in the San Cristobal Island https://github.com/NASUA/ZalophusPredatoryInteractions/archive/c9f28887dd94d5c9dac239ed23f9f92a6bbb8b11.zip 2021-11-13T04:42:10.101Z 770be4c86440edc567306f0d910303eabb4ac8ce4d19a46431c68385e1a34523 0.12.2<br> PHI-base/data Urban M, Cuzick A, Rutherford K, Irvine A, Pedro H, Pant R, Sadanadan V, Khamari L, Billal S, Mohanty S, Hammond-Kosack KE. PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database. Nucleic Acids Res. 2017 Jan 4;45(D1):D604-D610. doi: 10.1093/nar/gkw1089. Epub 2016 Dec 3. PMID:27915230 https://github.com/PHI-base/data/archive/55bdbb9105aeeafbd31e830a6bc18cc2afaa315e.zip 2021-11-13T04:47:07.815Z 9fb590efddf1ce872d382003568efb4bd43378991e6752b4818216840b22b7aa 0.12.2<br> ParasiteTracker/tick-interaction-database Seltmann, Katja C. 2020. Biotic species interactions about ticks manually extracted from literature. https://github.com/ParasiteTracker/tick-interaction-database/archive/09944e1a7283c2ff8514b1860e8299c527517040.zip 2021-11-13T04:42:33.097Z db8e1ea4e698ded1f7dbd6e74531899d8e02c78000887c80143776d653b6fe51 0.12.2<br> ParasiteTracker/vampire-moth-dwca Occurrence Records for vampire-moths-and-their-fruit-piercing-relatives. 2018-09-27. South Central California Network - 2ba077c1-aa41-455e-9a84-bccb61a91230. https://github.com/ParasiteTracker/vampire-moth-dwca/archive/c4549a1690b84595c88946f477057b9ab76e5360.zip 2021-11-13T04:42:37.906Z 5304518021dd435af41637132ad7629d464db3f8221a60f9e4cb89fddc28c0e9 0.12.2<br> ParasiteTracker/vampire-moths-and-their-fruit-piercing-relatives-Occurrence-Records Occurrence Records for vampire-moths-and-their-fruit-piercing-relatives. 2018-09-27. South Central California Network - 2ba077c1-aa41-455e-9a84-bccb61a91230. https://github.com/ParasiteTracker/vampire-moths-and-their-fruit-piercing-relatives-Occurrence-Records/archive/c4549a1690b84595c88946f477057b9ab76e5360.zip 2021-11-13T04:42:43.133Z 5304518021dd435af41637132ad7629d464db3f8221a60f9e4cb89fddc28c0e9 0.12.2<br> ThaoLe20/Bottlenose-Dolphin-Diet : Gime´nez J, Marc¸alo A, Ramı´rez F, Verborgh P, Gauffier P, Esteban R, et al. (2017) Diet of bottlenose dolphins (Tursiops truncatus) from the Gulf of Cadiz: Insights from stomach content and stable isotope analyses. PLoS ONE 12 (9): e0184673. https://doi.org/10.1371/journal. pone.0184673 https://github.com/ThaoLe20/Bottlenose-Dolphin-Diet/archive/c9ff689ba155ec0120532105b5f1c8e506c4cd11.zip 2021-11-13T04:48:38.813Z 759b2c7aad030f4c79835707da62b6c1f5f7ab58e06490d57d5e492b81f69086 0.12.2<br> ThaoLe20/Diet-of-bottlenose-dolphins : Gime´nez J, Marc¸alo A, Ramı´rez F, Verborgh P, Gauffier P, Esteban R, et al. (2017) Diet of bottlenose dolphins (Tursiops truncatus) from the Gulf of Cadiz: Insights from stomach content and stable isotope analyses. PLoS ONE 12 (9): e0184673. https://doi.org/10.1371/journal. pone.0184673 https://github.com/ThaoLe20/Diet-of-bottlenose-dolphins/archive/c9ff689ba155ec0120532105b5f1c8e506c4cd11.zip 2021-11-13T04:48:43.150Z 759b2c7aad030f4c79835707da62b6c1f5f7ab58e06490d57d5e492b81f69086 0.12.2<br> ThaoLe20/Fish-diets : Gime´nez J, Marc¸alo A, Ramı´rez F, Verborgh P, Gauffier P, Esteban R, et al. (2017) Diet of bottlenose dolphins (Tursiops truncatus) from the Gulf of Cadiz: Insights from stomach content and stable isotope analyses. PLoS ONE 12 (9): e0184673. https://doi.org/10.1371/journal. pone.0184673 https://github.com/ThaoLe20/Fish-diets/archive/c9ff689ba155ec0120532105b5f1c8e506c4cd11.zip 2021-11-13T04:48:47.560Z 759b2c7aad030f4c79835707da62b6c1f5f7ab58e06490d57d5e492b81f69086 0.12.2<br> ThaoLe20/Testing Jorrit H. Poelen. 2014. Species associations manually extracted from literature. https://github.com/ThaoLe20/Testing/archive/40a28dac110a264ad69c63c024ca11646f5f4250.zip 2021-11-13T04:48:56.823Z 7f4c77a3c4bd2218372929128ec6871c49364b0e6852ab628ad3f5e8022755cd 0.12.2<br> ThaoLe20/template-dataset Jorrit H. Poelen. 2014. Species associations manually extracted from literature. https://github.com/ThaoLe20/template-dataset/archive/40a28dac110a264ad69c63c024ca11646f5f4250.zip 2021-11-13T04:48:52.605Z 7f4c77a3c4bd2218372929128ec6871c49364b0e6852ab628ad3f5e8022755cd 0.12.2<br> TutoTestTuto/tutorial Pérez-Botello A M and Simões N (2019). Sponge-dwelling fauna from the Gulf of Mexico and the Caribbean sea a manually extracted from literature. https://github.com/TutoTestTuto/tutorial/archive/fea86a576396b139c65e0dbc7f8cca2f02cdde84.zip 2021-11-13T04:49:21.568Z c6430c995604d0edec3a05b678dddda5d3e0281c2a6c1b4f86319375cd2f4035 0.12.2<br> UCcongenomics/template-dataset Jorrit H. Poelen. 2014. Species associations manually extracted from literature. https://github.com/UCcongenomics/template-dataset/archive/ab8b030f16f4de01dc42c1c5669c629943dfec9a.zip 2021-11-13T04:49:26.219Z 0edd05ff80b5ca69d0d7a695ecee4a8e485fea2b6c2b555b011b7e09ee17da73 0.12.2<br> ZekeMarshall/ZMBioticInteractions Zeke Marshall. 2021. Species interactions manually extracted from literature. https://github.com/ZekeMarshall/ZMBioticInteractions/archive/8a2c1b0c5d40e115d06fe12d0d366ab5f2e2ca75.zip 2021-11-13T04:51:28.522Z 654e05ecf286db677fb8a6a9bc9daea8ace38724564f11e85f9c2c2934340745 0.12.2<br> abarner/template-dataset Jorrit H. Poelen. 2014. Species associations manually extracted from literature. https://github.com/abarner/template-dataset/archive/4bdb2493d4a6a9c36e864b1a2e3bab40459a1098.zip 2021-11-12T23:10:53.387Z e7410c21c897071619c1c444b5cc30662aa962362b8c916a0135e77d0536ba35 0.12.2<br> arw36/willoughby-etal-2017-roost-interactions Willoughby AR, Phelps KL, Olival KJ, Predict Consortium. A comparative analysis of viral richness and viral sharing in cave-roosting bats. Diversity. 2017 Sep;9(3):35. https://github.com/arw36/willoughby-etal-2017-roost-interactions/archive/05e08a5961d8c126103046a945dfea67ed20475b.zip 2021-11-12T23:11:04.388Z f2bce55ce35f646dd3d8714f7145d1dcf8478f609b57aecafc2194a81221e27a 0.12.2<br> arw36/willoughby-etal-2017-virus-interactions Willoughby AR, Phelps KL, Olival KJ, Predict Consortium. A comparative analysis of viral richness and viral sharing in cave-roosting bats. Diversity. 2017 Sep;9(3):35. https://github.com/arw36/willoughby-etal-2017-virus-interactions/archive/113064ba0e2cb6e16c290cffb5b4d2342f0aa728.zip 2021-11-12T23:11:09.257Z a5546a583e267d22cae305420804f16684115cf8d73b404b8877b738cc2eabe1 0.12.2<br> beraute/Klamath-mountains Genus level interactions from a metagenomic analysis of eDNA samples from the Klamath mountains https://github.com/beraute/Klamath-mountains/archive/2a885acccb9c7d8f0f368044d9ba71d74c309450.zip 2021-11-12T23:11:40.392Z 8bdedeb77ef6ec5be27937768adaf20d48671be636bffb79eb9d278d8bb666ed 0.12.2