register datasets with ODIS (using JSON-LD) #24
Comments
JSON-LD in ERDDAPPreviously I responded:
And now I'm seeing the JSON-LD embedded in the ERDDAP page, when you View Source: https://upwell.pfeg.noaa.gov/erddap/info/siocalcofiHydroBottle/index.html: <script type="application/ld+json">
{
"@context": "http://schema.org",
"@type": "Dataset",
"name": "CalCOFI SIO Hydrographic Bottle Data",
"headline": "siocalcofiHydroBottle"
...
}
</script>See full JSON-LD |
JSON-LD in OBIS
<script type="application/ld+json">
{
"@context": {
"@vocab": "https://schema.org/"
},
"@type": "Dataset",
"@id": "https://obis.org/dataset/d054afae-bb0c-484e-8658-d92b41ff9d7d",
"name": "CalCOFI and NMFS Seabird and Marine Mammal Observation Data, 1987-2006",
"description": "Original provider:\nPRBO Conservation Science\n\nDataset credits:\nThe projects were conducted under the grants awarded to the following \norganizations and their scientists.\n\nThe principle investigators of the CalCOFI part of this dataset are\n(in the chronological order from 1987 to 2006):\nRichard Veit and John McGowan, Scripps Institution of Oceanography (1987-1994)\nDavid Hyrenbach, Scripps Institution of Oceanography (1994-2000)\nBill Sydeman, PRBO Conservation Science (2000-2006)\n\nThe principle investigators of the Rockfish part of this dataset is\nBill Sydeman, PRBO Conservation Science (1996-2006)\n\n# the affiliations are the ones they belonged to at the time of the surveys.\n\nThe data were contributed by PRBO Conservation Science.\nThese two projects are on going. See [Supplemental information] for the \ninformation on the PIs and organizations in recent years.\n\nAbstract:\nThis dataset contains observation data of marine birds and mammals from California Cooperative Oceanic Fisheries Investigations (CalCOFI) from 1987-2006 and Rockfish cruises along the California coast from 1996-2006 by National Marine Fisheries Service (NMFS).\n\nData were collected aboard research vessels using standardized marine bird and mammal survey techniques (Tasker et al. 1984, Buckland et al. 1993). Marine birds \nand mammals were observed in a 90-degree arc from the bow to one side of the ship out to 300m. Counts are summarized by species and behavior along the transects in 3 km bins. Data span years 1987 - 2006.\n\nPurpose:\nRelating changing ocean productivity patterns and upper-trophic predator (seabirds and marine mammals) distributions to the underlying physical oceanographic variability enhances our understanding of the ecological context of the CalCOFI and NMFS database, thereby aiding in the interpretation of large-scale hydrographic and ocean productivity patterns. An inter-disciplinary, ecosystem-level perspective will provide new insight into offshore California wildlife habitat associations and how apex marine organisms (including fish with diets similar to seabirds and/or mammals) respond to differences in ocean climate, productivity, and water mass properties, information needed to manage fisheries and wildlife under changing ocean conditions.\n\nSupplemental information:\n[2020-09-30] The following invalid species names were corrected according to the Integrated Taxonomic Information System (ITIS).\nBlack-footed Albatross: Diomedea nigripes (174516) => Phoebastria nigripes (554379)\nBonaparte's Gull: Larus philadelphia (176839) => Chroicocephalus philadelphia (824040)\nCaspian Tern: Sterna caspia (176924) => Hydroprogne caspia (176935)\nElegant Tern: Sterna elegans (176925) => Thalasseus elegans (176931)\nFranklin's Gull: Larus pipixcan (176838) => Leucophaeus pipixcan (824082)\nGreat Egret: Casmerodius albus (174810) => Ardea alba (554135)\nLaughing Gull: Larus atricilla (176837) => Leucophaeus atricilla (824079)\nLaysan Albatross: Diomedea immutabilis (174517) => Phoebastria immutabilis (554378)\nLeast Tern: Sterna antillarum (176923) => Sternula antillarum (824127)\nRed Phalarope: Phalaropus fulicaria (554376) => Phalaropus fulicarius (176734)\nRoyal Tern: Sterna maxima (176922) => Thalasseus maximus (824142)\nSouth Polar Skua: Catharacta maccormicki (176801) => Stercorarius maccormicki (660062)\nWillet: Catoptrophorus semipalmatus (176638) => Tringa semipalmata (824147)\nParula americana (178868) => Setophaga americana (950033)\nDendroica petechia T(178878) => Setophaga petechia (950039)\nDendroica townsendi (178897) => Setophaga townsendi (950058)\nDendroica occidentalis (178902) => Setophaga occidentalis (950059)\nDendroica coronata (178891) => Setophaga coronata (950046)\nWilsonia pusilla (178973) => Cardellina pusilla (950080)\n\n[UPDATE 2013-03-25] The following species codes had been associated with invalid species names. These were corrected to valid species names.\nWWSC White-Winged Scoter => Melanitta fusca deglandi\nSTAL Short-Tailed Albatross => Phoebastria albatrus\nLAAL Laysan Albatross => Diomedea immutabilis\nLETU Leatherback Turtle => Dermochelys coriacea\nThese data are publicly available without restriction. However, it is\nsuggested that potential users contact the data contributor (Marine\nDivision Director at PRBO Conservation Science, [email protected])\nor PI Bill Sydeman ([email protected]) for questions concerning \nthe use of dataset (methods, accuracy, help with interpretation etc.).\n\n\nThe dataset is also available at <a href=\"http://oceaninformatics.ucsd.edu/datazoo/\">Ocean Informatics Data Zoo</a> \n(http://oceaninformatics.ucsd.edu/datazoo/).\n\nThe CalCOFI and Rockfish projects are on going.\nThe Principle Investigators of these projects are as follows (listed those in \nrecent years only):\n\nRockfish survey\n2008, Leg 1/2: Bill Sydeman, Farallon Institute for Advanced Ecosystem Research\n2008, Leg 3: Jaime Jahncke, PRBO Conservation Science\n2009, Leg 1/2: Bill Sydeman, Farallon Institute for Advanced Ecosystem Research\n2009, Leg 3: Jaime Jahncke, PRBO Conservation Science\n\nCalCOFI survey\n2006-2007: Bill Sydeman, PRBO Conservation Science\n2007-current: Bill Sydeman, Farallon Institute for Advanced Ecosystem Research\n\nThese recent data are available from these individuals or organizations upon request.\nThe recent data by Bill Sydeman will be also available through OBIS-SEAMAP in the \nnear future.\n\n\nEach sighting is a total of all of the birds/mammals of that species and behavior \nseen in an area (approx. 3 km long and 300m wide). The location is represented at \nthe middle of the bin. Length may be less at the end of a transect, and width \nmay be less depending on the weather.\nEach bin is temporally about 10 minutes in duration (depending on ship speed).\n\nTracklines on this map represent on-effort only. Off-effort tracks may be obtained \nfrom the data provider.",
"url": "https://obis.org/dataset/d054afae-bb0c-484e-8658-d92b41ff9d7d",
"sameAs": [
"http://ipt.env.duke.edu/resource?r=zd_507"
],
"license": "This work is licensed under a Creative Commons Attribution Non Commercial (CC-BY-NC) 4.0 License",
"citation": "Sydeman, W. 2015. CalCOFI and NMFS Seabird and Marine Mammal Observation Data, 1987-2006. Data downloaded from OBIS-SEAMAP (http://seamap.env.duke.edu/dataset/507) on yyyy-mm-dd.",
"version": "2021-04-24T09:53:50.000Z",
"keywords": [
"Occurrence,Marine Animal Survey,Marine Biology,Marine mammals,Seabirds,Sea turtles,Vessel,Visual Sighting",
"Observation",
"Occurrence"
],
"variableMeasured": [],
"includedInDataCatalog": {
"@id": "https://obis.org",
"@type": "DataCatalog",
"url": "https://obis.org"
},
"temporalCoverage": "1987/2006",
"distribution": {
"@type": "DataDownload",
"contentUrl": "https://ipt.env.duke.edu/archive.do?r=zd_507",
"encodingFormat": "application/zip"
},
"spatialCoverage": {
"@type": "Place",
"geo": {
"@type": "GeoShape",
"polygon": "-126.474237 29.77212,-126.474237 40.091331,-117.2345 40.091331,-117.2345 29.77212,-126.474237 29.77212"
},
"additionalProperty": {
"@type": "PropertyValue",
"propertyID": "http://dbpedia.org/resource/Spatial_reference_system",
"value": "http://www.w3.org/2003/01/geo/wgs84_pos#lat_long"
}
},
"provider": [
{
"@id": "https://oceanexpert.org/institution/19393",
"@type": "Organization",
"legalName": "Duke University",
"name": "Duke University",
"url": "https://oceanexpert.org/institution/19393"
}
]
}
</script> |
JSON-LD in EDI
Hmm... there are 2 JSON-LD entries:
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Google Dataset SearchIt's also very interesting to find 71 datasets in Google's Dataset Search that combs the entire internet for these JSON-LDs. https://datasetsearch.research.google.com/search?query=calcofi ERDDAP Dataset in the Google Dataset Catalog |
Institute identifier? OceanExpert or ROROceanExpertThe recommendation from OBIS has been to use identifiers in OceanExpert for people and institutions. I don't see an institute for CalCOFI when I search "calcofi" in OceanExpert.org, but I do see:
Research Organization Registry (ROR)Whereas OceanExpert is marine focused, GBIF and NOAA are embracing the newer global Research Organization Registry (ROR) at ROR.org. For instance, see parent-child relationships: I learned about this through the MBON DMAC group: |
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And querying for "calcofi" on Google Dataset Search, there are:
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ODIS CatalogueBut only 6 datasets show on https://catalogue.odis.org/search
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Here are the existing dataset repositories that "should" be generating JSON-LD already: Dataset Repositories with CalCOFI Datasets1. ERDDAP (n=21 today)Gridded or tabular data, including oceanographic data. (Other ERDDAP servers exist.) 2. OBIS (n=5 today)Biogeographic data as DarwinCore 3. EDI (n=3 today)Full dataset record with flexible dataset structure. Part of DataOne network. |
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I created a Quarto notebook in our workflows repo to generate the datasets
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Hi Jeff and all, Thanks for the support! Exciting that CalCOFI will be a featured example and working towards OBIS and EOV inclusion. Per our convo, I just updated:
Details with code are in: Cheers, Ben PS Attached is the transcript with AI generated Action Items and Summary. |
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From @evsatt:
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