Batch Editing for Specify 7

We have made much use of Batch Editing in Specify 6. It is necessary for us to be able to transition to Specify 7.

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This is a feature we would welcome as well in Specify 7.

Batch Edit is a required feature for our workflow as well. We use this tool for quickly adding data to multiple records at once and also quality control. It would be even more useful if Batch Edit capabilities were expanded to include additional tables.

We also need batch editing in Specify7 for several of our institutions, especially those that cannot use Specify6 due to technical reasons.

Hi all,

Could you share with us examples of workflows you are using with the BatchEdit tool? We are discussing implementation and development of batch editing in Specify 7.

We use Batch Edit to help standardize and fill in missing Geography data. This is especially useful when we have many specimens with similar Locality Names, but varying levels of Geography data available on the specimen labels & database records. We conduct Georeferencing based on units in the Geography tree; when there is too much missing data in the Locality, we don’t georeference them in our typical workflow.

For example, we have many specimens with the Locality Name ‘Lake Sunapee, N.H.’, and the lake is actually on the border between Merrimack and Sullivan Counties. Without further research, these specimens are transcribed with the State and Locality name, but no County. In Batch Edit, we can add County and get these records into our typical georeferencing workflow.


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Hi Grant,

In addition to resolving duplicate localities with (numerous!) spellings and typos, we often clear up inconsistencies for easier searching. For example, the “verbatim locality” for many specimens may have been listed in one place, but was entered by sundry volunteers with different lots in different ways. One example:

These are a few items from one collecting event at one locality; “Verb Locality” needs to be the same (the Locality Names also need to be resolved).

Note that I already resolved hundreds of these in this donation using batch editing. Another example:

These are all the same locality. They do not necessarily need the same “Verb Locality”, but adding collector and collection date to the query would allow grouping them by the same verbatim location.

Thanks,

Larry J. Van Stone

Data and Mollusk Specialist

Delaware Museum of Nature and Science

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I also echo the request by gholman that additional tables be made accessible to batch editing. Ideally, it would include ALL tables, but I know that the deeper in a schema a query reaches, the longer the SQL gets, so the programmers will probably need to take this in stages.

Here’s an example of a use case where we need support for additional tables in Batch Edit.

Specifically, Lithostratigraphy (LS) and Chronostratigraphy (CS).

In this example we the UMich Paleo Invertebrate database, where data has been entered in the Remarks table that would be better captured in CS:Series/Epoch, LS:Litho Group, LS:Formation, and or LS:Member.

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Similar example to what @gholman has above. Sometimes historically, things have been entered into the remarks field that could best be put elsewhere. By being able to export certain tables/fields as a spreadsheet, edit them through regex/code, and then re-upload into Specify, we can progressively improve data quality. Or perhaps a researcher comes to us with a spreadsheet with measurements for items within the collection, it is much easier to keep them in spreadsheet format and make bulk edits than having to go through one by one in the form system.

My personal opinion of the best/easiest way to implement this would be to allow edits to be made through the workbench by just going through the normal upload workflow, but with a switch called “enable overwrites” or something similar.

We would love to see this. Our example is adding more data to existing records.

I would also like to be able to batch edit more tables. For example, we do large annual DNA sequencing runs and while create the DNA records manually while selecting tissues to sequence, once the results come in it would be very handy to use the Batch editor to update those records with BOLD identifiers, the actual sequences, target markers, etc. Batch edit for the DNA sequences isn’t available in Specify6

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I’ve been adding and correcting information in the collecting event table. Sometimes the information was wrong in the original import of the specimens, and sometimes there is new information from the field notebooks that had not been digitized before. I have been also cleaning up mistakes and typos.

I do this editing directly in the database because it’s not practical for me to use Specify 6 at the moment, but I would much prefer to do all editing in Specify 7.

What @markp suggest with the Workbench sounds good.