Monday, March 23, 2020

Darwin Core Million promo: best and worst

Bob mesibovThe following is a guest post by Bob Mesibov.
There's still time (to 31 March) to enter a dataset in the 2020 Darwin Core Million, and by way of encouragement I'll celebrate here the best and worst Darwin Core datasets I've seen.
The two best are real stand-outs because both are collections of IPT resources rather than one-off wonders.

The first is published by the Peabody Museum of Natural History at Yale University. Their IPT website has 10 occurrence datasets totalling ca 1.6M records updated daily, and I've only found minor data issues in the Peabody offerings. A recent sample audit of the 151,138 records with 70 populated Darwin Core fields in the botany dataset (as of 2020-03-18) showed refreshingly clean data:
  • entries correctly assigned to DwC fields
  • no missing-but-expected entry gaps
  • consistent, widely accepted vocabularies and formatting in DwC fields
  • no duplicate records
  • no character encoding errors
  • no gremlin characters
  • no excess whitespace or fancy alternatives to simple ASCII characters
The dataset isn't perfect and occurrenceRemarks entries are truncated at 254 characters, but other errors are scarce and easily fixed, such as
  • 14 records with plant taxa mis-classified as animals
  • 4 records with dateIdentified earlier than eventDate
  • minor pseudo-duplication in several fields, e.g. "Anna Murray Vail; Elizabeth G. Britton" and "Anne Murray Vail; Elizabeth G. Britton" in recordedBy
  • minor content errors in some entries, e.g. "tissue frozen; tissue frozen" and "|" (with no other characters in the entry).
I doubt if it would take more than an hour to fix all the Peabody Museum issues besides the truncation one, which for an IPT dataset with 10.5M data items is outstanding. There are even fields in which the Museum has gone beyond what most data users would expect. Entries in vernacularName, for example, are semicolon-separated hierarchies of common names: "dwarf snapdragon; angiosperms; tracheophytes; plants" for Chaenorhinum minus.

The second IPT resource worth commending comes from GBIF Portugal and consists of 108 checklist, occurrence record and sampling event datasets. As with the Peabody resource, the datasets are consistently clean with only minor (and scattered) structural, format or content issues.

The problems appearing most often in these datasets are "double-encoding" errors with Portugese words and no-break spaces in place of plain spaces, and for both of these we can probably blame the use of Windows programs (like Excel) at the contributing institutions. An example of double-encoding: the Portugese "prôximo" is first encoded in UTF-8 as a 2-byte character, then read by a Windows program as two separate bytes, then converted back to UTF-8, resulting in the gibberish "prôximo". A large proportion of the no-break spaces in the Portugese datasets unfortunately occur in taxon name strings, which don't parse correctly and which GBIF won't taxon-match.

And the worst dataset? I've seen some pretty dreadful examples from around the world, but the UK's Natural History Museum sits at the top of my list of delinquent providers. The NHM offers several million records and a disappointingly high proportion of these have very serious data quality problems. These include invalid and inappropriate entries, disagreements between fields and missing-but-expected blanks.

Ironically, the NHM's data portal allows the visitor to select and examine/download records with any one of a number of GBIF issues, like "taxon_match_none". Further, for each record the data portal reports "GBIF quality indicators", as shown in this screenshot:

Clicking on that indicator box gives the portal visitor a list of the things that GBIF found wrong with the record (a list that overlaps incompletely with the list I can find with a data audit). I'm sure the NHM sees this facility differently, but to me it nicely demonstrates that NHM has prioritised Web development over data management. The message I get is
"We know there's a lot wrong with our data, but we're not going to fix anything. Instead, we're going to hand our mess as-is to any data users out there, with cleverly designed pointers to our many failures. Suck it up, people."
In isolation NHM might be seen as doing what it can with the resources it has. In a broader context the publication of multitudes of defective records by NHM is scandalous. Institutions with smaller budgets and fewer staff do a lot better with their data — see above.


If your institution is closed and you have spare work-from-home time, consider doing some data cleaning. For those not afraid of the command line, I've archived the websites A Data Cleaner's Cookbook (version 2) and its companion blog BASHing data (first 100 posts) in Zenodo with local links between the two, so that the two resources can be downloaded and used offline in any Web browser.

Tuesday, March 03, 2020

The 2020 Darwin Core Million

Bob mesibovThe following is a guest post by Bob Mesibov.

You're feeling pretty good about your institution's collections data. After carefully tucking all the data items into their correct Darwin Core fields, you uploaded the occurrence records to GBIF, the Atlas of Living Australia (ALA) or another aggregator, and you got back a great report:

  • all your scientific names were in the aggregator's taxonomic backbone
  • all your coordinates were in the countries you said they were
  • all your dates were OK (and in ISO 8601 format!)
  • all your recorders and identifiers were properly named
  • no key data items were missing

OK, ready for the next challenge for your data? Ready for the 2020 Darwin Core Million?

How it works

From the dataset you uploaded to the aggregator, select about one million data items. That could be, say, 50000 records in 20 populated Darwin Core fields, or 20000 records in 50 populated Darwin Core fields, or something in between. Send me the data for auditing before 31 March 2020 as a zipped plain-text file by email to, together with a DOI or other identifier for their online, aggregated presence.

I'll audit datasets in the order I receive them. If I can't any find data quality problems in your dataset, I'll pay your institution AUD$150 and declare your institution the winner of the 2020 Darwin Core Million here on iPhylo. (One winner only; datasets received after the first problem-free dataset won't be checked.)

If I find data quality problems, I'll let you know by email. If you want to learn what the problems are, I'll send you a report detailing what should be fixed and you'll pay me AUD$150. At 0.3-0.75c/record, that's a bargain compared to commercial data-checking rates. And it would be really good to hear, later on, that those problems had indeed been fixed and corrected data had been uploaded to the aggregator.

What I look for

For a list of data quality problems, see this page in my Data Cleaner's Cookbook. The key problems are:

  • duplicate records
  • invalid data items
  • data items in the wrong fields
  • data items inappropriate for their field
  • truncated data items
  • records with items in one field disagreeing with items in another
  • character encoding errors
  • wildly erroneous dates or coordinates
  • incorrect or inconsistent formatting of dates, names and other data
  • items

If you think some of this is just nit-picking, you're probably thinking of your data items as things for humans to read and interpret. But these are digital data items intended for parsing and managing by computers. "Western Hill" might not be the same as "Western Hill" in processing, for example, because the second item might have a no-break space between the words instead of a plain space. Another example: humans see these 22 variations on collector names as "the same", but computers don't.

You might also be thinking that data quality is all about data correctness. Is Western Hill really at those coordinates? Is the specimen ID correct? Is the barely legible collector name on the specimen label correctly interpreted? But it's possible to have entirely correct digital data that can't be processed by an application, or moved between applications, because the data suffer from one or more of the problems listed above.

I think my money is safe

The problems I look for are all easily found and fixed. However, as mentioned in a previous iPhylo post, the quality of the many institutional datasets that I've sample-audited ranges from mostly OK to pretty awful. I've also audited more than 100 datasets (many with multiple data tables) for Pensoft Publishers, and the occurrence records among them were never error-free. Some of those errors had vanished when the records had been uploaded to GBIF, because GBIF simply deleted the offending data items during processing (GBIF, bless 'em, also publish the original data items).

Neither institutions nor aggregators seem to treat occurrence records with the same regard for detail that you find in real scientific data, the kind that appear in tables in scientific journal articles. A comparison with enterprise data is even more discouraging. I'm not aware of any large museum or herbarium with a Curator of Data on the payroll, probably because no institution's income depends on the quality of the institution's data, and because collection records don't get audited the way company records do, for tax, insurance and good-governance purposes.

So there might be a winner this year, but I doubt it. Maybe next year. ALA has a year-long data quality project underway, and GBIF Executive Secretary Joe Miller (in litt.) says that GBIF is now paying closer attention to data quality. The 2021 Darwin Core Million prize could be yours...