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NCEAS-DF-semantic-annotations-review

Overview of currently annotated data packages within the Arctic Data Center (as of 2020-10-12) in preparation for the 2020 NSF site visit, plus workflows to update datapackages with additional semantic annotations.

Overview

In order to improve data discoverablity within the Arctic Data Center (ADC), the datateam is working to implement semantic search within the respository. Here, we explore progress to date (Oct 2020). Data and analyses are detailed below. For a summarized report, see here (though this needs updating).

In addition to recent efforts by the ADC data team to add semantic annotations to each incoming dataset (beginning ~Aug 2020, as a part of the data curation workflow), there are legacy data that can be enhanced by retroactively adding semantic annotations to dataset attributes. Here, we also explore non-annotated attributes across the ADC corpus, identify 'cryptically-named' attributes (i.e. attributes whose names/descriptions may not provide sufficient information for understanding the what the attribute is a measurement of), and manually assign appropriate semantic annotation URIs (drawing from ECSO, the Ecosystem Ontology). We then develop a workflow for automating this batch-update of legacy ADC datapackages with semantic annotations.

Getting Started

Scripts are numbered in the order of analyses.

Repository Structure

NCEAS-DF-semantic-annotations-review
  |_code
  | |_assign_URIs_to_nonannotated_attributes
  | |_batchUpdate_functions
  | |_old
  |_data
  | |_aggregate_scores
  | |_filtered_term_counts
  | | |_nonannotated_attributes2020-10-01
  | | |_nonannotated_attributes2020-10-12
  | |_outputs
  | | |_attributes_to_annotate
  | | | |_script_10a2_attributes_to_annotate
  | |_queries
  | | |_query2020-10-01
  | | | |_query2020-10-12
  | | | |_query2020-10-12_attributes_from_nonannotated_datapackages
  | |_unnested_tokens
  | | |_nonannotated_attributes2020-10-01
  | | |_nonannotated_attributes2020-10-12
  |_docs
  |_dump_files
  |_eml
  |_figures

Code

For a summary of each script and the outputs generated, see workflow_notes.

Data

The following dataset contains all attributes (and corresponding infomation) that are to be semantically annotated using the batch-update workflow (scripts 10a.1-10b)

data/outputs/attributes_to_annotate/script10a2_attributes_to_annotate/attributes_to_annotate_2021Mar12.csv

  • identifier: unique persistent identifier assigned to each ADC data package (in most cases, this is a DOI)
  • entityName: The name of an entity (e.g. dataTable, spatialVector, etc.)
  • attributeName: The name of an attribute, as listed in a .csv file
  • attributeLabel: A descriptive label that can be used to display the name of an attribute
  • attributeDefinition: Longer description of the attribute, including the required context for interpreting the attributeName
  • attributeUnit: Unit string for affiliated attribute
  • viewURL: URL of ADC data package
  • query_datetime_utc: date/time of query
  • assigned_valueURI: term URI from ECSO that has been manually assigned to the corresponding attribute and is to be applied as its semantic annotation
  • prefName: the preferred name of a semantic annotation; scraped from the web
  • ontoName: the ontology that an semantic annotation comes from; scraped from the web
  • package_type: can be one of the following: standalone, child, parent, WEIRD, MULTINESTING, too long to load; see workflow_notes (under Script: 10a.2_batch_update_data_wrangling.R) for a description of these package_types
  • child_rm: only available if package_type == "child"; the resource map of the child package
  • parent_rm: only present if package_type == "child"; the resource map of the parent package
  • parent_metadata_pid: only present if package_type == "child"; the metadata pid of the parent package
  • status: notes whether a datapackage has already has some number semantic annotations, or if it has never been annotated before; (a) "dp has at least one annotation", (b) "dp was never annotated"
  • isPublic: TRUE, FALSE, or NA; denotes whether or not a datapackage is public
  • num_datasets: number of data objects (dataTables or otherEntities) that are contained in the datapackage
  • update_cat: category of datapackage for subsetting batch update runs (standaloneDOI, standaloneUUID, childDOI, childUUID, parentDOI, WEIRDDOI, )

Software

These analyses were performed in R (version 3.6.3). See SessionInfo for dependencies.

Acknowledgements

Work on this project was supported by: ...