Data Quality Toolkit 2024: Difference between revisions
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This page was inspired by Bob Mesibov's [https://www.datafix.com.au/cookbook/ Data Cleaner's Cookbook], GBIF's [https://data-blog.gbif.org/post/issues-and-flags/ data quality flags], and iDigBio's [https://github.com/iDigBio/idigbio-search-api/wiki/Data-Quality-Flags data quality flags]. | This page was inspired by Bob Mesibov's [https://www.datafix.com.au/cookbook/ Data Cleaner's Cookbook], GBIF's [https://data-blog.gbif.org/post/issues-and-flags/ data quality flags], and iDigBio's [https://github.com/iDigBio/idigbio-search-api/wiki/Data-Quality-Flags data quality flags]. | ||
If you already know which tool or CMS you are using to clean your data, you can visit a tool- and CMS-specific toolkit: [[Arctos Data Quality Toolkit|Arctos]], [[Excel Data Quality Toolkit|Excel]], [[OpenRefine Data Quality Toolkit|OpenRefine]], [[Specify Data Quality Toolkit|Specify]], [[ | If you already know which tool or CMS you are using to clean your data, you can visit a tool- and CMS-specific toolkit: [[Arctos Data Quality Toolkit|Arctos]], [[Excel Data Quality Toolkit|Excel]], [[OpenRefine Data Quality Toolkit|OpenRefine]], [[Specify Data Quality Toolkit|Specify]], [[https://biokic.github.io/symbiota-docs/editor/quality/ Symbiota]], [[TaxonWorks Data Quality Toolkit|TaxonWorks]]. | ||
== Catalog Numbers and Other Identifiers== | == Catalog Numbers and Other Identifiers== | ||
Revision as of 12:34, 21 March 2024
Overview
This page was created to aggregate common data quality issues and potential solutions to those issues in collection management systems and CMS-agnostic tools. Data quality issues are grouped into data categories, and links to resources for identifying and fixing the issues are provided.
This page was inspired by Bob Mesibov's Data Cleaner's Cookbook, GBIF's data quality flags, and iDigBio's data quality flags.
If you already know which tool or CMS you are using to clean your data, you can visit a tool- and CMS-specific toolkit: Arctos, Excel, OpenRefine, Specify, [Symbiota], TaxonWorks.
Catalog Numbers and Other Identifiers
Duplicate Catalog Numbers
Problem: The same catalog number is used multiple times within your dataset. (This problem may or may not be intentional, depending on your collection's policies. It is generally best to not duplicate catalog numbers, when possible).
Solutions:
Dates
Date Hasn't Happened Yet
Problem: The date the specimen was identified, collected (often designated using the eventDate field), or georeferenced is in the future.
Solutions:
Date is Suspiciously Old
Problem: The date the specimen was identified, collected (often designated using the eventDate field), or georeferenced is outside the expected historical date range. The expected date range depends on the institution, but it is unlikely that most collections have specimens with dates prior to 1600.
Solutions:
Identified Date Earlier than Collected Date
Problem: The date the specimen was identified (dateIdentified field) is earlier than the date the specimen was collected (eventDate).
Solutions:
Year, Month, and Day Values Do Not Match Date
Problem: The event year, month, and day values do not match the provided event date. The event date is often the date of collection for preserved specimens.
Solutions:
Geography
Coordinates are Zero
Problem: The provided latitude and longitude values are 0.
Solutions:
Coordinates Do Not Fall Within Named Geographic Unit
Problem: The provided coordinates do not fall within the geographic boundaries of the named country, state, and/or county.
Solutions:
Georeference Metadata with no Associated Georeference
Problem: Metadata fields regarding coordinates, such as coordinateUncertaintyInMeters, georeferenceProtocol, georeferenceSources, georeferencedBy, georeferenceRemarks, and geodeticDatum are provided, but no coordinates are present. This is sometimes intentional, particularly when georeferencedBy and georeferencedRemarks are used to indicate whether a record was purposefully not georeferenced. However, it is rare that the other metadata fields can be used without associated coordinates (i.e., decimalLatitude, [ https://dwc.tdwg.org/terms/#dwc:decimalLongitude decimalLongitude], or verbatimCoordinates).
Solutions:
Elevation is Unlikely
Problem: Elevation values are either too high (>17000 m) or too low (-11000 m) to occur on Earth.
Solutions:
Improperly Negated Latitudes/Longitudes
Problem: The sign of the latitude (decimalLatitude) or longitude (decimalLongitude) does not match the sign/hemisphere of the given country. For example, all longitudes in the U.S. should be negative.
Solutions:
Invalid Coordinates
Problem: Coordinates deviate from accepted ranges or formats, like decimalLatitude and decimalLongitude exceeding -90 to 90 and -180 to 180, respectively. verbatimCoordinates have to be valid values for coordinates in decimal degrees, degrees decimal minutes, degrees minutes second.
Solutions:
Lower Geography Values are Provided, but No Higher Geography
Problem: Lower geography (e.g., county, state/province) values exist, but no higher geography values (e.g., country) are provided.
Solutions:
Minimum and Maximum Elevation Values Mismatched
Problem: The minimum elevation (minimumElevationInMeters) has a greater value than the maximum elevation (maximumElevationInMeters).
Solutions:
Mismatched Country and CountryCode Values
Problem: The provided value for country and countryCode do not match.
Solutions:
Mismatched Geographic Terms
Problem: A record has lower geographic terms (e.g., state/province, county) that do not exist under the provided higher geographic term(s). For example, country = Canada and stateProvince = Sussex. There is no Sussex province in Canada.
Solutions:
Missing Geodetic Datum
Problem: Geodetic datum is a key piece of a properly georeferenced specimen, but is usually left blank. Although it is commonly assumed to be in ‘WGS84’, this should be added and noted as such.
Solutions:
Missing Latitudes/Longitudes
Problem: A record has a latitude value, but not a longitude value, or vice versa.
Solutions:
Misspelled Geographic Unit Names
Problem: The geographic units (e.g., country, state/province, county) are misspelled, resulting in poor matching of geographic unit names to existing geographic lists.
Solutions:
Taxonomy
Misspelled or Invalid Taxonomic Names
Problem: Scientific names are misspelled, resulting in poor matching of taxonomic names to taxonomic databases.
Solutions:
Unknown Higher Taxonomy
Problem: Species may be missing higher taxonomic information.
Solutions:
Other Issues
Incorrect Character Encodings
Problem: Data inconsistencies arise when incorrect character encodings are used during data manipulation or transfer. This issue occurs when datasets are opened, downloaded, or imported across different software platforms, leading to misinterpretation and garbled text. For instance, special characters like accents or symbols may be rendered incorrectly, affecting the readability and accuracy of the data. (e.g., Carl Linné).
Solutions:
Incorrect Line Endings
Problem: When transferring text files between Unix/Linux and DOS/Windows systems, line endings can become inconsistent. Unix/Linux systems typically use line feed (LF) characters, while DOS/Windows systems use carriage return (CR) and line feed (LF) combinations. This mismatch can result in extra characters appearing in the data, causing visual artifacts and processing errors.
Solutions:
Invalid Individual Count
Problem: individualCount values may not make sense as a positive integer.
Solutions:
Non-standardized BasisOfRecord Values
Problem: Values in the BasisOfRecord field do not match the recommended controlled vocabulary. While using standardized terms in this field is not strictly necessary, doing so does improve the discoverability and interoperability of your data.
The currently accepted values for BasisOfRecord include: MaterialEntity, PreservedSpecimen, FossilSpecimen, LivingSpecimen, MaterialSample, Event, HumanObservation, MachineObservation, Taxon, Occurrence, MaterialCitation.
Note that even punctuation and capitalization differences in these values (e.g., Preserved Specimen) are discouraged.
Solutions: