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3 results for “DataONE”
Results of semantic queries for "carbon cycling" for datasets in the DataONE catalog
DataONE (https://www.dataone.org) is a federation of institutions involved with the earth and environmental sciences that share data through common cyberinfrastructure. In 2016, the DataONE project carried out a quantification of the utility of semantic query, by measuring the precision and recall of relevant datasets available through that catalog. Precision is defined as the proportion of relevant data in the retrieved results, and recall is the proportion of relevant data retrieved, compared to all relevant data present in the repository (see Methods). This dataset contains the queries and results of that study. Four data tables are included. First, a table of the 10 queries, which were formatted in several ways, including natural language and text strings (for plain text searches of various parts of metadata), and URIs for measurements in the EcoSystem Ontology (ECSO). A second table contains 994 relevant datasets in the DataONE catalog, with a column for each of the ten queries and boolean value indicating whether the dataset is a match for that query. Two query results tables are included, for the raw and summarized results of the query tests. A fifth entity contains the zipped code (R language) used to perform the queries in the DataONE system. When run against approximately 1000 datasets (in October, 2016), results for the ten queries ranged from 0-50% (precision) and 0-100% (recall), indicating that traditional searches may sometimes be adequate to return all relevant data in a corpus, but results can be erratic and inconsistent, with potentially large returns of irrelevant data in the result set. When querying through semantic classes, precision and recall were much higher and more consistent (90-100% and 75-100%, respectively).
Mapping EDI, NEON and DataONE units to the QUDT ontology, 2022
In the metadata of digital environmental datasets, automated processing is hindered by the wide variety of representations for unit that may be human-readable, but may not be unambiguous or machine-interpretable, (e.g., grams per square meter, gm/m2, g/m2, gm-2, g/m^2, g.m-2, g m-2 and gramPerMeterSquared). Matching disparate representations of the same unit into a single unit concept from an ontology assists with interpretation and reuse by providing a linkage to a complete unit definitions with label, description, dimensions. Datasets with shared units can be identified during searches, and are more suitable for automating analyses and potential transformation. This dataset contains data and code associated with a project to map units in ecological metadata collected between 2013 and 2022 by DataONE, the Environmental Data Initiative and the U.S. National Ecological Observatory Network to the QUDT ontology using successive string transformations. Data entities include a) raw metadata as received (355,057 unit instances) b) integrated raw data c) substitution tables for string transformations d) resulting lookup table for 896 distinct units matched to QUDT units e) associated R code used for QUDT matching plus a web service and R functions for adding annotation elements to Ecological Metadata Language metadata documents. Using these substitutions and code, 91% of unit instances in the raw metadata could be matched to QUDT. Data and results are discussed in “Porter JH, M O’Brien, M Frants, S Earl, M Martin, C Laney. (in review) Using a Units Ontology to Annotate Pre-Existing Metadata. Submitted to Scientific Data.
A biodiversity dataset graph: DataONE
<p>A biodiversity dataset graph: DataONE</p> <p>The intended use of this archive is to facilitate (meta-)analysis of the Data Observation Network for Earth (DataONE). DataONE is a distributed infrastructure that provides information about earth observation data.</p> <p>This dataset provides versioned snapshots of the DataONE network as tracked by Preston [2] between 2018-11-06 and 2020-05-07 using "preston update -u https://dataone.org".</p> <p>The archive consists of 256 individual parts (e.g., preston-00.tar.gz, preston-01.tar.gz, ...) to allow for parallel file downloads. The archive contains three types of files: index files, provenance logs and data files. In addition, index files have been individually included in this dataset publication to facilitate remote access. Index files provide a way to links provenance files in time to establish a versioning mechanism. Provenance files describe how, when, what and where the DataONE content was retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543 . </p> <p>To retrieve and verify the downloaded DataONE biodiversity dataset graph, first concatenate all the downloaded preston-*.tar.gz files (e.g., cat preston-*.tar.gz > preston.tar.gz). Then, extract the archives into a "data" folder. Alternatively, you can use the preston[2] command-line tool to "clone" this dataset using:</p> <p>$ java -jar preston.jar clone --remote https://zenodo.org/record/3849494/files</p> <p>After that, verify the index of the archive by reproducing the following provenance log history:</p> <p>$ java -jar preston.jar history<br> <0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .<br> <hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> <http://purl.org/pav/previousVersion> <hash://sha256/8c67e0741d1c90db54740e08d2e39d91dfd73566ea69c1f2da0d9ab9780a9a9f> .<br> <hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> <http://purl.org/pav/previousVersion> <hash://sha256/3ed3acaca7ac57f546d0b8877c1927ab5e08c23eccaa8219600c59c77a72c685> .<br> <hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> <http://purl.org/pav/previousVersion> <hash://sha256/857753997a7595a1b372b05641b58a25d9408b7ff08d557ce1fe8b73e4bd383f> .<br> <hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> <http://purl.org/pav/previousVersion> <hash://sha256/7ee0376f4c3f7aeeda36927a5211395e5da8201e810e8c7e638a0fe23d001e88> .<br> <hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> <http://purl.org/pav/previousVersion> <hash://sha256/68b4974d8ab7c4c7a7a4305065839b60ba460aaa862590b34c67877738feba90> .<br> <hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> <http://purl.org/pav/previousVersion> <hash://sha256/060a76d56255bf9482c951748c91291fddeeb20f180632132be1344e081b2372> .<br> <hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> <http://purl.org/pav/previousVersion> <hash://sha256/29357bdfab4548025f8a5743301f5c3c9146fa436c39e3c9e019fb9409ac9c42> .<br> <hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> <http://purl.org/pav/previousVersion> <hash://sha256/3669cd95100d1d533eb8953ff4ec5092cbd8addb8879b3e6262191148a8a3ebb> .<br> <hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> <http://purl.org/pav/previousVersion> <hash://sha256/8dc1663299359d271cb1b4c14ad521d0f1be67743689dd18016543dc1e097efb> .<br> <hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807> <http://purl.org/pav/previousVersion> <hash://sha256/dc4903e8afee651db1d9bf509f20503bf9c8e89679c4bcffb46d5b97440cb6de> .<br> <hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7> <http://purl.org/pav/previousVersion> <hash://sha256/f3bed9db3092c744604df5f50248a2ec36e564fe78a65f45c4190283bd61c807> .<br> <hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650> <http://purl.org/pav/previousVersion> <hash://sha256/e3c7b3b14b2b792e3e2e560a1b2bef059ac93f777dee616b836317bc9cbfcbf7> .<br> <hash://sha256/87de0898919d2212977a586965e930ae45bdd1366073591c808c208a635e2814> <http://purl.org/pav/previousVersion> <hash://sha256/631a4531e7bb052816d28454bbeec3428d5e7bfd1f148c4f21ce63a6cf86c650> .<br> <hash://sha256/79ec3ee370a0d38311bc352af07a36380cd3aa04dc98154cf723bbc73d12ee77> <http://purl.org/pav/previousVersion> <hash://sha256/87de0898919d2212977a586965e930ae45bdd1366073591c808c208a635e2814> .<br> <hash://sha256/e54b360a4ca84a4503e4c10a8a8cca062c130be7429c8fe6ea1e0e82fe113e12> <http://purl.org/pav/previousVersion> <hash://sha256/79ec3ee370a0d38311bc352af07a36380cd3aa04dc98154cf723bbc73d12ee77> .<br> <hash://sha256/2910f784f84e112f124a56ce54bd06b76e510f90276629d2d144ce29e326d80f> <http://purl.org/pav/previousVersion> <hash://sha256/e54b360a4ca84a4503e4c10a8a8cca062c130be7429c8fe6ea1e0e82fe113e12> .<br> <hash://sha256/bcb0bdff0689cfb06f586d057703e41d1c6ba409867232217081dd8cb5053c87> <http://purl.org/pav/previousVersion> <hash://sha256/2910f784f84e112f124a56ce54bd06b76e510f90276629d2d144ce29e326d80f> .<br> <hash://sha256/a12f8c7fbf4fbfa71536c7e1b2614a35454dac6a7fe9e1cc0b4df41ab2269bef> <http://purl.org/pav/previousVersion> <hash://sha256/bcb0bdff0689cfb06f586d057703e41d1c6ba409867232217081dd8cb5053c87> .<br> <hash://sha256/2b5c445f0b7b918c14a50de36e29a32854ed55f00d8639e09f58f049b85e50e3> <http://purl.org/pav/previousVersion> <hash://sha256/a12f8c7fbf4fbfa71536c7e1b2614a35454dac6a7fe9e1cc0b4df41ab2269bef> .</p> <p>To check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.</p> <p>$ java -jar preston.jar verify<br> hash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945 file:/home/preston/preston-dataone/data/e5/5c/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945 OK CONTENT_PRESENT_VALID_HASH 21580 hash://sha256/e55c1034d985740926564e94decd6dc7a70f779a33e7deb931553739cda16945<br> hash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f file:/home/preston/preston-dataone/data/d0/dd/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f OK CONTENT_PRESENT_VALID_HASH 2035 hash://sha256/d0ddcc2111b6134a570bcc7d89375920ef4d754130cecc0727c79d2b05a9f81f<br> hash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53 file:/home/preston/preston-dataone/data/47/2d/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53 OK CONTENT_PRESENT_VALID_HASH 1935 hash://sha256/472de9d1c9fd7e044aac409abfbfff9f12c6b69359df995d431009580ffb0f53<br> hash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687 file:/home/preston/preston-dataone/data/b2/98/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687 OK CONTENT_PRESENT_VALID_HASH 1553 hash://sha256/b29879462cd43862129c5cf9b149c41ecd33ffef284a4dbea4ac1c0f90108687</p> <p><br> Note that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston".</p> <p>Files in this data publication:</p> <p>--- start of file descriptions ---</p> <p>-- description of archive and its contents (this file) --<br> README</p> <p>-- executable java jar containing preston[2] v0.1.15. --<br> preston.jar</p> <p>-- preston archives containing DataONE data files, associated provenance logs and a provenance index --<br> preston-[00-ff].tar.gz</p> <p>-- individual provenance index files --<br> 2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a<br> 2aecaf289def0e23a27058bf7715f226ef9189905f0be13228174825633125cf<br> 2f65ae542401d4c2daf1bca70de640211da6749188f67d28ea71acd7d8ba070b<br> 35eb1e17e2bf3e71212cde35bdb03e8a6545a57483ea3c1633929257b70cf637<br> 3d38b70198e448674be6a63d14b9817f3a956f48bba7418fa7baa086a56c05b7<br> 66ad3e5e904740f1e835ac6718dda4279e0c24b204ea0d1113cda1352a5072ba<br> 7466a35e42dea7e2be068060ec0c926f9a8686388ed504ef5c6c990c1ba4e8d0<br> 81161d9746c2a5823641c436e773fb4508516b055da85f4494b38c545349da39<br> 8bf062872ce958545d361e9d53a552ffb025ac29ab875caad1157c0995d34f66<br> a90eed8d70c54c8e554f2dfde4fceb434eda162d9615d62de96ded2344f88a78<br> c33ef5e29100b323412f1f3bc66908c8e01e4f0d1db4ea3685d2fffc47981dd6<br> c84dffef20fec958255e759db6445fc469d73695674a33ae6f7e567a088c9fe0<br> d362d599d72000c4feb464db5a669b12e15fc3ca1a49b1e7d4d6f7d6d5d15411<br> d9378616636be3686bbabd5bf29d50f0ef0e5ceb5ddd7dfce47f7e755b596b7d<br> da26fa6e7371385ed3f61af9a766221c833060d59dfd4869bbd7110f95f288db<br> e4103a75627857de3ee2e317429108611c244fc448c01d1d7bf652115c3b8a55<br> eb368fedb8f100210dd968edcf80f4d13cab3dd64135a6ab744102cf15e68c94<br> f13ab4bca04f894ae8eabb51fa01b4dfbc69f717eabc9896c728e2ba39c4db27<br> f493baf276892a199a0b0d078359f64a38fe8ad3f807921f8d41ef73f7343b1f<br> ff92b6c06ae5286bd2f1db679e0fcc4da294acb9bc01b2e9522378d99218c2e3</p> <p>--- end of file descriptions ---</p> <p><br> References</p> <p>[1] Data Observation Network for Earth (DataONE, https://dataone.org) accessed from 2018-11-06 to 2020-05-07 with provenance hash://sha256/2b5c445f0b7b918c14a50de36e29a32854ed55f00d8639e09f58f049b85e50e3.<br> [2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .</p> <p><br> This work is funded in part by grant NSF OAC 1839201 from the National Science Foundation.</p>
ScienceDex guides
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