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Help & How To

This is where you’ll find a variety of guides, tutorials, and FAQs for publishing data and using the VertNet Portal. Don’t forget to check Training Workshops and Publications & Videos for other descriptive and educational materials. We haven't forgotten about developers either. If all else fails, contact us with your questions.

While many institutions list stomach contents in the following Darwin Core terms, not many denote if it is preserved or saved with the words "preserved" or "saved."

These three Darwin Core terms listed above are only available via full text searching, so with that in mind, I tried using exact phase in the Search Options window, http://portal.vertnet.org/search?advanced=1. Exact phrase requires you to place quotes around the exact phrase you are typing. I used the Darwin Core field Class to narrow to Aves.

  1. This query identifies records with the exact phrase “stomach contents” while narrowing the class = Aves.
    Results > 10k records*: http://portal.vertnet.org/search?q=%22stomach+contents%22+class:Aves
  2. This query identifies records with the exact phrase “stomach contents saved” while narrowing the class = Aves.
    Results = 155 records*: http://portal.vertnet.org/search?q=%22stomach+contents+saved%22+class:Aves
  3. This query identifies records with the exact phrase “stomach contents preserved” while narrowing the class = Aves.
    Results = 3 records*: http://portal.vertnet.org/search?q=%22stomach+contents+preserved%22+class:Aves

The second query might be a good place to start with 155 records* across approximately 10 institutions as it specifically addresses the question at hand.

The first query still could be useful in viewing records to find how institutions are noting the specimen stomach contents.

In an effort to further reduce the first query, I continued looking at records and confirmed with an Ornithology Curator, that stomach contents are preserved in ethanol. So by adding ethanol to the search options in Any of these words, I was able to reduce the query that was producing >10k down to 5,032 records*.
http://portal.vertnet.org/search?q=%22stomach+contents%22+class:Aves+(ethanol)

Since we are using exact phrase, you can also experiment with "stomach content" and get some different results. In the case of primarily MSB and MVZ which have >600 records* between the two in this example, they use a standard format with stomach content and an ethanol percentage in the preparations field. Sometimes, but not always, they list "stomach contents" in the dynamicProperities or the occurrenceRemarks fields as well. So putting that all together with an OR in the exact phrase field, I can bring back 5,120 records*.
http://portal.vertnet.org/search?q=%22stomach+content%22+OR+%22stomach+contents%22+class:Aves+(ethanol)

Now, it is possible that other preparations might be preserved in ethanol, while still listing stomach contents and might not serve the question at hand, but a greater amount of these records are now records with preserved stomach contents.

Any of these queries could still be further narrowed by using an institutionCode or adding genus or specificEphithet to the criteria.

* Record counts may not be exact as listed in examples due to availability of data in the portal.

The "Has Tissue" filter is dependent on the following words being present in the preparations field:

tissuetokens = ["tiss", "tissue", "blood", "dmso", "dna", "extract", "froze", "frozen", "freez", "freeze", "heart", "muscle", "higado", "kidney","liver", "lung", "nitrogen", "pectoral", "rinon", "rnalater", "sample", "sangre", "toe", "spleen"]"

If a collection has not published this information in their preparations field, their data will not return when using the filter.

If you know a collection with tissues that does not return when using the tissue filter, you can use a combination of the Darwin Core term institutionCode and exact phrase in the Search Options window, http://portal.vertnet.org/search?advanced=1, to find that data instead. Exact phrase requires you to place quotes around the exact phrase you are typing.

For example, the Sam Noble Oklahoma Museum of Natural History (OMNH) publishes a Genomic Resources Collection, but does not publish specific preparations within the data.

With that in mind, I was able to search their tissue data using exact phrase="genomic" and instituionCode=OMNH.
Results >10k records*: http://portal.vertnet.org/search?q=%22genomic%22+institutioncode:OMNH

This query could be further narrowed by using additional criteria in the Search Options window like class or genus or specificEphithet to the criteria.

This query narrows using genus=Accipiter and specificEpithet=cooperii.
Results = 8 records*: http://portal.vertnet.org/search?q=%22genomic%22+specificepithet:cooperii+genus:Accipiter+institutioncode:OMNH

* Record counts may not be exact as listed in examples due to availability of data in the portal.

The following is an excerpt from the VertNet Norms for Data Use and Publication.

Preferred Citations

In the absence of a citation practice that takes precedence, we recommend the following preferred formats to use when citing data published through VertNet. Square brackets denote values that must be obtained either from records within a dataset or from the description of the dataset. A glossary of terms used in square brackets is given at the end of the Preferred Citations section.

Single dataset

General Format
[dataset name]. [data publisher]. [link to dataset] (accessed on [date])
Example
Cowan Tetrapod Collection at the University of British Columbia Beaty Biodiversity Museum (UBCBBM). University of British Columbia. http://ipt.vertnet.org:8080/ipt/resource.do?r=ubc_bbm_ctc_birds (accessed on 2014-07-28)

Aggregated data (from multiple datasets)

Cite each data publisher in the aggregate using the single dataset citation format described above.

Example
Cowan Tetrapod Collection at the University of British Columbia Beaty Biodiversity Museum (UBCBBM). University of British Columbia. http://ipt.vertnet.org:8080/ipt/resource.do?r=ubc_bbm_ctc_birds (accessed on 2014-07-28)
Field Museum of Natural History (Zoology) Bird Collection. Field Museum. http://fmipt.fieldmuseum.org:8080/ipt/resource.do?r=fm_birds (accessed on 2014-07-28)
University of Kansas Bird Collection. University of Kansas Biodiversity Institute. http://ipt.nhm.ku.edu/ipt/resource.do?r=kubi_ornithology (accessed on 2014-07-28)

Single specimen/observation record

VertNet includes the text of a record citation in the bibliographicCitation field in the record itself for all data publishers who provide this information. If the record has a value in the bibliographicCitation field, construct the full citation by appending information about the date the data were accessed. If the record does not contain a value for bibliographicCitation, use the appropriate format described below.

If the bibliographicCitation is provided in the record:
[bibliographicCitation] (accessed on [date])
Example
urn:catalog:CM:Herps:105730. Carnegie Museum of Natural History Herpetology Collection. Carnegie Museums. http://ipt.vertnet.org:8080/ipt/resource.do?r=cm_herps (accessed on 2014-07-28)
If there is no bibliographicCitation, but occurrenceID is provided in the record:
[occurrenceID]. [dataset name]. [data publisher]. [link to dataset] (accessed on [date])
Example
urn:catalog:CM:Herps:105730. AMNH Mammal Collection. American Museum of Natural History. http://ipt.vertnet.org:8080/ipt/resource.do?r=amnh_mammals (accessed on 2014-07-28)
If there is no bibliographicCitation or occurrenceID provided in the record:
[catalogNumber]. [dataset name]. [data publisher]. [link to dataset] (accessed on [date])
Example
105730. Field Museum of Natural History (Zoology) Bird Collection. Field Museum. http://fmipt.fieldmuseum.org:8080/ipt/resource.do?r=fm_birds (accessed on 2014-07-28)

Where can I find the elements to create a citation?

All the elements can be found in fields contained within downloaded records or in the description of the dataset (i.e., the metadata) from which the record originates:

  • [bibliographicCitation]: in the field bibliographicCitation in the record.

  • [occurrenceID]: in the field occurrenceID in the record.

  • [catalogNumber]: in the field catalogNumber in the record.

  • [dataset name]: This is listed as the Resource Citation (under Citations) in the dataset metadata (published as an EML file in a Darwin Core archive) and can also be found under Citation on the Rights tab in the record detail in the VertNet portal. If the Resource Citation is missing, use the Title of the resource in the dataset metadata, also found under Resource on the Rights tab in the record detail in the VertNet portal.

  • [data publisher]: This is listed as the Organisation in the dataset metadata and under Organisation on the Rights tab in the record detail in the VertNet portal. It is not in downloaded records.

  • [link to dataset]: in the field [dataSource] in the record. If dataSource is missing, use the Source URL on the Rights tab in the record detail in the VertNet portal.