globalbioticinteractions/elton

Access, review and index existing species interaction datasets

Welcome to Global Biotic Interactions (GloBI)

The mission of this project is to find efficient ways to normalize and integrate species interaction data to enable researchers and enthusiasts to answer questions like: Which species does an Angel Shark ( Squatina squatina ) eat in the Gulf of Mexico?

Please see https://globalbioticinteractions.org or https://github.com/globalbioticinteractions/globalbioticinteractions/wiki for more information.

Citing GloBI

Poelen, J. H., Simons, J. D., & Mungall, C. J. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics, 24, 148–159. doi:10.1016/j.ecoinf.2014.08.005

Licenses

Unless otherwise noted, source code is released under GLPv3 and data is available under Creative Commons Attribution 4.0 International License. We are trying to do the best we can to ensure that the references to the original data sources are preserved and attributed. If you feel that there are better ways to do this, please let us know.

elton's Issues

transitive dependency commons-lang3 causes class cast exception

See https://github.com/globalbioticinteractions/virus-host-db/runs/4206440928?check_suite_focus=true .

review [local]... |�/�-�\�|�-�\�|�/�-�\�|�-�\�|�/�-�\�|�-�\�|�/�-�\�|�-�\�|�/�-�\�|�-�\�|�/�-�\�|�-�\�|�/�-�\�|�-�\�|�/�-�\�|�-�\�|�/�-�\�|�-�\�|�java.lang.ClassCastException: class [Ljava.lang.Object; cannot be cast to class [Ljava.lang.String; ([Ljava.lang.Object; and [Ljava.lang.String; are in module java.base of loader 'bootstrap')
at org.eol.globi.service.TaxonUtil.generateTaxonName(TaxonUtil.java:593)
at org.eol.globi.service.TaxonUtil.generateTargetTaxon(TaxonUtil.java:709)
at org.eol.globi.service.TaxonUtil.enrichIfNeeded(TaxonUtil.java:754)
at org.eol.globi.service.TaxonUtil.enrichTaxonNames(TaxonUtil.java:727)
at org.eol.globi.process.TaxonNameEnricher.on(TaxonNameEnricher.java:34)
at org.eol.globi.process.InteractionListenerImpl.on(InteractionListenerImpl.java:71)
at org.eol.globi.data.TableInteractionListenerProxy.on(TableInteractionListenerProxy.java:40)
at

support local dataset registries

Currently, elton supports finding datasets through github and zenodo.

Suggest to introduce local folders (e.g., cache and/or dataset directories) as specific registries, so that we can say:

$ elton interactions --registries local

or

$ elton interactions --registries cache

to point to local directories that contain one or more dataset and related resources.

add reviewer and review date to ```elton check``` report

add reviewer and review date column to elton check report.

reviewer	review date
elton v0.1.3: your friendly GloBI sidekick	2019-01-01T00:10:10Z

localityId / localityName not exposed via "elton interactions"

to reproduce:

run elton interactions on github.com/globalbioticinteractions/refuted-interaction-data produces:

decimalLatitude	decimalLongitude	localityId	localityName
57.0182	-3.3922

while the original has:

localityId	localityName	decimalLatitude	decimalLongitude
GEONAMES:2651429	River Dee, Aberdeenshire, Scotland	57.0182	-3.3922

use cache remote dependencies when running elton checks on local datasets

Currently, elton check is able to run checks on local and remote species interaction datasets. Currently, remote dependencies of local datasets are not cached. This prevents testing on datasets that require non-streaming or local access to dependencies.

Proposed is to locally cache remote dependencies when testing local datasets.

allow for elton to use zip archive as cache dir.

Currently, you tell elton to use a specific cache dir by saying:

elton ls --cache-dir=some/folder/

however, some publications use an archive zip of the cached datasets, so suggest to also support:

elton ls --cache-dir=some/archive.zip 

This way, you can more easily work with immutable collections of datasets.

consider review note categories

Currently, review notes are human readable messages. When creating review reports, categorization of review notes might be handy to answer questions like: "How many date parsing issues were found?"

For now, categorization can be done using simple test filter (e.g., grep "failed to parse"). However, a more structured approach using categories (e.g. category "date parsing" with detailed message like "failed to parse [197-01-01] using pattern [YYYY-mm-DD]"). See also https://github.com/frictionlessdata/goodtables.io/blob/d235660855298fe09e777b79cb314f0e1f58442d/frontend/spec.json can be introduced if needed.

overly eager github workflow review configuration

When using elton init ... to generate a GloBI index configuration, a default github review action is configured in an automatically generated file:

.github/workflows/review.yml

name: GloBI review by Elton

on:
  push:
    branches: [ '*' ]
  pull_request:
    branches: [ '*' ]
  schedule:
    - cron: "* * * * 1"
...

Unfortunately, the line cron: "* * * * 1" triggers review every minute on Mondays.

Suggest to change to: cron: "0 0 * * 1" to trigger a review on Monday at midnight according to the local server's clock.

proposal to improve generated nanopub

@mdmtrv suggested to update the currently generated nanopubs along the lines of:

https://github.com/mdmtrv/nanopub-example-collection/blob/main/examples/pensoft-openbiodiv/globalbioticinteractions_bees-1-revised.trig (see also below)

@prefix this: <http://purl.org/np/RA0006bkysPoHYsZDgl2A-Iq8tOpuWqLSflN7KLeb8jGI> .
@prefix sub: <http://purl.org/np/RA0006bkysPoHYsZDgl2A-Iq8tOpuWqLSflN7KLeb8jGI#> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix pav: <http://swan.mindinformatics.org/ontologies/1.2/pav/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix prism: <http://prismstandard.org/namespaces/basic/2.0/> .
@prefix nomen: <http://purl.obolibrary.org/obo/NOMEN> .
@prefix openbiodiv: <http://openbiodiv.net/> .
@prefix dwc: <http://rs.tdwg.org/dwc/terms/> .
@prefix dwciri: <http://rs.tdwg.org/dwc/iri/> .
 
sub:Head {
  this: np:hasAssertion sub:Assertion;
    np:hasProvenance sub:Provenance;
    np:hasPublicationInfo sub:Pubinfo;
    a np:Nanopublication .
}
 
sub:Assertion {
  sub:Interaction obo:RO_0000057 sub:Organism_1, sub:Organism_2;
    a obo:GO_0044419 .
   
  sub:Organism_1 obo:RO_0002622 sub:Organism_2;
    rdfs:label "Lasioglossum mosselinum" ;
    rdf:type dwc:Organism;
    dwc:identificationID sub:Identification_1.
     
  sub:Identification_1 dwciri:toTaxon sub:ScName_1.
 
  sub:ScName_1 rdf:type nomen:NOMEN_0000036;
    dwc:genus "Lasioglossum";
    dwc:specificEpithet "mosselinum".   
   
  sub:Organism_2 rdfs:label "Compositae" ;
    rdf:type dwc:Organism;
    dwc:identificationID sub:Identification_2.
     
  sub:Identification_2 dwciri:toTaxon sub:ScName_2.
 
  sub:ScName_2 rdf:type nomen:NOMEN_0000036;
    dwc:genus "Compositae".
 
  sub:TaxonomicConcept_2 openbiodiv:scientificName sub:ScName_2;
                dwc:taxonID "6070956";
                rdf:type dwc:Taxon.
}
 
sub:Provenance {
  sub:Assertion prov:wasDerivedFrom sub:JournalArticle.
 
  sub:JournalArticle a fabio:JournalArticle;
             dc:title "Capalictus, a new subgenus of Lasioglossum Curtis, 1833 from South Africa, with description of three new species (Hymenoptera, Apoidea, Halictidae).";
             prism:publicationDate "2012"^^xsd:year;
             prism:doi "https://doi.org/10.5852/ejt.2012.28".
             dcterms:bibliographicCitation "Pauly, A., J. Gibbs and M. Kuhlmann. 2012. Capalictus, a new subgenus of Lasioglossum Curtis, 1833 from South Africa, with description of three new species (Hymenoptera, Apoidea, Halictidae). European Journal of Taxonomy 28: 1-28" .
   
}
 
sub:Pubinfo {
  this: dcterms:license <https://creativecommons.org/licenses/by/4.0/>;
    pav:createdBy <https://doi.org/10.5281/zenodo.1212599>;
    prov:wasDerivedFrom <https://doi.org/10.5281/zenodo.229519> .
   
  <https://doi.org/10.5281/zenodo.229519> dcterms:bibliographicCitation "Eardley C, Coetzer W. 2011. Catalogue of Afrotropical Bees. http://doi.org/10.15468/u9ezbh" .
}

fyi @tkuhn

support [elton init] command to help auto-generate GloBI configurations

Currently, you have to clone an existing GloBI [github] data repository like https://github.com/globalbioticinteractions/template-dataset .

To support auto-generating GloBI config for indexing an existing dataset without having to rely on some github template, we can introduce something similar to "git init" (the command that helps create an empty github repo) :

$ elton init --data-url=https://example.org/data.tsv --data-citation "Jane Doe. 2020. My interaction data" 

executing this default command would make elton to have a peek at the data.tsv, guess its data format and generate files like README.md, .travis.yaml, globi.json and .gitignore with appropriate generated content.

@seltmann @qgroom curious to hear your thoughts on this Elton functionality if you have any.

add support for Preston provenance tracking / archives

Currently, Elton is using a built-in provenance tracking of biodiversity datasets.

Suggested is to add support for Preston archives / provenance tracking.

elton working with sqlite

@seltmann suggested to show an example of how to use elton's review or interaction reports with SqlLite.

Issue with report JSON

@jhpoelen I noticed that the reports are causing spreadsheets to hang up (even small reports). When I looked at the dataContext it might have a malformed JSON with starting { and closing }}

c64c7fea-78f8-4e4b-8758-3dd15122e4bb 2020-04-26T22:10:13Z GloBI automated reviewer (elton-0.9.5) local note found unsupported interaction type with id: [http://purl.obolibrary.org/obo/RO_0008504] and name: [parasitized by] Seltmann, Katja C. 2020. Biotic species interactions about bees (Anthophila) manually extracted from literature.. Accessed at file:///home/travis/build/seltmann/bee-interaction-database/./ on 26 Apr 2020. {"reviewId":"c64c7fea-78f8-4e4b-8758-3dd15122e4bb","reviewDate":"2020-04-26T22:10:13Z","reviewerName":"GloBI automated reviewer (elton-0.9.5)","reviewCommentType":"note","reviewComment":"found unsupported interaction type with id: [http://purl.obolibrary.org/obo/RO_0008504] and name: [parasitized by]","namespace":"local","context":{"argumentTypeId":"https://en.wiktionary.org/wiki/support","interactionTypeId":"http://purl.obolibrary.org/obo/RO_0008504","interactionTypeName":"parasitized by","referenceCitation":"Eickwort, G. C. (1981). Aspects of the Nesting Biology of Five Nearctic Species of Agapostemon (Hymenoptera: Halictidae).Journal of the Kansas Entomological Society,54(2), 337351. Retrieved from www.jstor.org/stable/25084166","resourceLineNumber":"126","resourceURI":"file:/home/travis/build/seltmann/bee-interaction-database/./datasets/local/118a90198e32a93388010dbdb929751310f7f961855afc23c9b5cb914288ce64","sourceTaxonId":"https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=757556","sourceTaxonName":"Agapostemon sericeus","studySourceCitation":"Seltmann, Katja C. 2020. Biotic species interactions about bees (Anthophila) manually extracted from literature.. Accessed at file:///home/travis/build/seltmann/bee-interaction-database/./ on 26 Apr 2020.","studyTitle":"localEickwort, G. C. (1981). Aspects of the Nesting Biology of Five Nearctic Species of Agapostemon (Hymenoptera: Halictidae).Journal of the Kansas Entomological Society,54(2), 337351. Retrieved from www.jstor.org/stable/25084166","targetBodyPartId":"http://purl.obolibrary.org/obo/ENVO_00005803","targetBodyPartName":"nest","targetTaxonId":"https://www.gbif.org/species/1343377","targetTaxonName":"Nomada articulata"}}

allow for disabling of progress reporter

By default, Elton provides a progress reporter in the form of a "/-|" ASCII art spinner.

When running Elton as a service (e.g., systemd), this progress reporter shows up in the systemd log with entries like "[149B blob data]". Suggest to introduce an option to disable progress logging.

Apr 07 17:40:39 Ubuntu-1804-bionic-64-minimal systemd[1]: Starting Elton tracks species interaction datasets...
Apr 07 17:41:13 Ubuntu-1804-bionic-64-minimal elton[10055]: [149B blob data]
Apr 07 17:41:15 Ubuntu-1804-bionic-64-minimal elton[10055]: [128B blob data]

expose claim type (e.g., refute / support)

With globalbioticinteractions/globalbioticinteractions#376 , GloBI provides a way to support and refute specific interactions. Elton does not yet expose this in it's elton interactions table.

support update using URLs instead of namespaces

Currently, namespace (e.g., globalbioticinteractions/ucsb-izc) are used to update individual datasets using:

$ elton update globalbioticinteractions/ucsb-izc

where the namespace is available from list provided via elton ls after a full update elton update.

However, in the background, these namespaces are translated to github repositories (or their Zenodo counterparts) (e.g., https://github.com/globalbioticinteractions/ucsb-icz).

Suggest to directly support:

$ elton update https://github.com/globalbioticinteractions/ucsb-icz

fyi @seltmann

create template repository for creating TPT reporting using R and Sqlite

@seltmann suggested to create a runnable example of how to create TPT report confirm with Kat's reporting template.

show what information was used to infer some interaction type

e.g.,

scientificName: bee
associatedTaxa: plant

GloBI currently silently maps this to:

source taxon: bee
interaction type: interactsWith
target taxon: plant

Suggest to make this inference explicit like:

1. GloBI used associated taxa field to infer the interaction type to be interactsWith
2. GloBI used associated taxa field to infer the target taxon name to be "plant"
   etc.

create a "head" review - containing only first x of each review note type

To get a glimpse of what is in a review, we'd like to have a limited set of representative review notes.

Currently, we have:

elton review > review.tsv

which creates all the review notes.

We'd like to have:

elton review -n100 > review.tsv

which creates up to 100 review notes per review type-comment.

For instance, if there's 200 notes that say "sourceTaxonName missing" and 500 that say "targetTaxonName missing", then

elton review -n100 > reviewFirst100.tsv

would contains 201 rows: a header, first 100 notes of sourceTaxonName missing, for 10 notes of targetTaxonName missing.

parasite tracker webpage index and review limit by collection

@jhpoelen the review "buttons" on the parasite tracker page link to the reviews of the datasets that those collections are contained, but are not of the individual collection. Possible to limit to the specific collection.

BYU is on scan (globalbioticinteractions/scan) can the index and review buttons only show those records with institutionCode=BYU and collectionCode=BYUC. I can fill out the collection codes in the parasitetracker.tsv for reference.

--

Using elton interactions from a DwC URL

Hi @jhpoelen

following what we have discussed about indexing biotic interactions from GBIF, I have some questions which may demand adding new features do elton. Let's see.

I'm using the following command to get all DwC-Archives from deeplinerk.bio:

preston ls --remote https://deeplinker.bio/c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55 --log tsv --no-cache | grep 'application/dwca' | cut -f1

It gives me a list of URL's of DwC-Archives:

http://tb.plazi.org/GgServer/dwca/1C546649D866E731FF8B2771487AD818.zip
http://tb.plazi.org/GgServer/dwca/E376FF8EFFF1F22C326D1E0DFF8BFFDF.zip
https://nzobisipt.niwa.co.nz/archive.do?r=westpac_chromis
https://nzobisipt.niwa.co.nz/archive.do?r=nearshorereeffishes
https://nzobisipt.niwa.co.nz/archive.do?r=mpi_tag

Now, I trying to extract interaction data from these archives using elton:

preston ls --remote https://deeplinker.bio/c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55 --log tsv --no-cache | grep 'application/dwca' | cut -f1 | elton interactions

c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55 is the hash of the latest bio graph.

But the way which elton works (as far I know) I need run elton init before passing the --data-url and --data-citation to create the globi.json file and then set format: "dwca".

I'm wondering if there is some way to skip elton init and use elton interactions to extract all interactions from the dwca's.

Maybe then I can do something like

preston ls --remote https://deeplinker.bio/c253a5311a20c2fc082bf9bac87a1ec5eb6e4e51ff936e7be20c29c8e77dee55 --log tsv --no-cache | grep 'application/dwca' | cut -f1 | elton interactions | awk -F\t '$27!=""'

the awk -F\t '$27!=""' is appended to the command in order to get only "complete" interactions records, since elton will output records with empty targetTaxonName (field number 27) when it can't find any interactions (the DwC-A doest not contains any data for associatedTaxa for example).

In parallel, I'm editing the scripts in https://github.com/bio-guoda/preston-scripts to store these DwC-A into a AWS EMR facilty.

Additionally, for the kind of analysis that I'm trying to do, will be interest to know in which DwC fields the interactions are stored (associatedTaxa, associatedOccurrence, ResourceRelationship). Is there any way to get that information too?

thanks.

add header to [elton check] tsv output

suggest using review_summary for review on https://www.globalbioticinteractions.org/parasitetracker/

@jhpoelen Presently the review is not as comprehensive as the updated review_summary. Suggest to replace with review_summary, if possible.

verbatimInteractionName not in indexed-interactions.tsv

@jhpoelen Can we add it to the https://www.globalbioticinteractions.org/parasitetracker indexted-interactions.tsv? Using elton 0.9.5

unexpected results from recent big-bee review

Hi @jhpoelen I was doing the quarterly review of Big Bee contributors and I am getting some unexpected results where UCSB is not showing any bee interactions and only a few other interactions.

elton --version 0.12.5

datasets under review:

EMTuckerLabUMMZ/ummzi
globalbioticinteractions/asu-asuhic
globalbioticinteractions/cas-ent
globalbioticinteractions/emec
globalbioticinteractions/fsca
globalbioticinteractions/ku-semc
globalbioticinteractions/lacm-lacmec
globalbioticinteractions/mcz
globalbioticinteractions/sdnhm-sdmc
globalbioticinteractions/ucm-ucmc
globalbioticinteractions/ucsb-izc
globalbioticinteractions/unhc-unhc

review summary file is truncated and review_summary_by_collection does not have as many interactions as seen at https://depot.globalbioticinteractions.org/reviews/globalbioticinteractions/ucsb-izc/README.txt

review_summary_by_collection.txt
review_summary.txt

Thanks!

indexing of globalbioticinteractions/saproxylic fails with java.lang.NoClassDefFoundError: Could not initialize class org.apache.jena.rdf. model.ModelFactory

when running elton names globalbioticinteractions/saproxylic -

listing taxa [globalbioticinteractions/saproxylic]... java.lang.NoClassDefFoundError: Could not initialize class org.apache.jena.rdf.
model.ModelFactory
at org.eol.globi.data.DatasetImporterForSaproxylic.importStudy(DatasetImporterForSaproxylic.java:61)
at org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:65)
at org.globalbioticinteractions.elton.cmd.CmdUtil.handleSingleNamespace(CmdUtil.java:99)
at org.globalbioticinteractions.elton.cmd.CmdUtil.lambda$handleNamespaces$1(CmdUtil.java:74)
at org.globalbioticinteractions.elton.cmd.CmdUtil.handleNamespaces(CmdUtil.java:45)
at org.globalbioticinteractions.elton.cmd.CmdUtil.handleNamespaces(CmdUtil.java:68)
at org.globalbioticinteractions.elton.cmd.CmdNames.run(CmdNames.java:37)
at org.globalbioticinteractions.elton.cmd.CmdNames.run(CmdNames.java:26)
at org.globalbioticinteractions.elton.cmd.CmdLine.run(CmdLine.java:15)
at org.globalbioticinteractions.elton.cmd.CmdLine.run(CmdLine.java:24)
at org.globalbioticinteractions.elton.Elton.main(Elton.java:15)

include catalogNumber, institutionCode and collectionCode for source/target records

when using elton interactions, the DwC catalog number, institution code, and collection code should be included in addition to the already included DwC occurrence id.

include record information related to ```elton check``` validation test report

elton check is used to run a validation/compatibility check on interaction datasets. Now, the tsv formatted reports look like:

local	file:///home/travis/build/globalbioticinteractions/scan/
>= 500 unique messages, turning off logging.
local	found unsupported interaction type [anacardiaceae]
local	found unsupported interaction type [associated with]
local	found unsupported interaction type [cactaceae]
local	found unsupported interaction type [cupressaceae]
local	found unsupported interaction type [euphorbiaceae]
local	found unsupported interaction type [ex]
local	found unsupported interaction type [eza/zza 1]
local	found unsupported interaction type [h]
local	found unsupported interaction type [host]
local	found unsupported interaction type [larrea]
local	found unsupported interaction type [larval foodplant]
local	found unsupported interaction type [pinaceae]
local	found unsupported interaction type [platanaceae]
local	found unsupported interaction type [reared ex caenothus herbaceous recv]
local	found unsupported interaction type [reared ex cercis canadensis lot]
local	found unsupported interaction type [reared ex]
local	invalid date string [0000-00-00]
local	invalid date string [1896-00-00]
...

suggested to include context (e.g. record, line numbers, archive name) to help more easily find suspicious records in datasets.

inspired by globalbioticinteractions/scan#2 .

report total total number of records examined

Currently, elton reports the number of interaction records.

Desired is to have elton report the number of total records examined (see ParasiteTracker/tpt-reporting#8 (comment)).

order bag of properties in review context

currently, elton includes a json representation of the review report generated by:

elton review

e.g.,

{
  "reviewId": "c183e9aa-7390-436a-aa7a-af5426745f19",
  "reviewDate": "2020-03-31T00:07:17Z",
  "reviewerName": "GloBI automated reviewer (elton-0.3.5-SNAPSHOT)",
  "reviewCommentType": "note",
  "reviewComment": "date [2105-06-09T00:00:00Z] is in the future",
  "namespace": "globalbioticinteractions/squamatabase",
  "context": {
    "prey": "Aspidoscelis costata",
    "interactionTypeNameVerbatim": "preys on",
    "interactionTypeName": "preysOn",
...
  }
}

Suggest to order the context properties alphabetically to make it easier for humans to find properties by name.

tsv/csv report reduce number of files

Need in the archive:

1. summary file, 2) file that shows errors, 3) file with full report (errors + confirmation that record was indexed properly), 4) name report

So I think this means:
Keep review-note.tsv, review-summary.tsv, interactions.tsv, names.tsv in the archive

remove review-info.tsv, review-full.tsv from the archive for now.

tsv/csv report summary.tsv add unique interactions

Review summary is great. I would also like to see a list of the unique interactions used in my dataset (help me find errors).

unexpected results on running ```elton interactions``` twice on local dataset

Currently, when running:

elton interactions twice on a local dataset without pre-existing elton cache (e.g., in datasets/ folder), the following is observed on running the command the second time.

$ elton interactions
argumentTypeId	sourceOccurrenceId	sourceCatalogNumber	sourceCollectionCode	sourceCollectionId	sourceInstitutionCode	sourceTaxonId	sourceTaxonName	sourceTaxonRank	sourceTaxonPathIds	sourceTaxonPath	sourceTaxonPathNames	sourceBodyPartId	sourceBodyPartName	sourceLifeStageId	sourceLifeStageName	sourceSexId	sourceSexName	interactionTypeId	interactionTypeName	targetOccurrenceId	targetCatalogNumber	targetCollectionCode	targetCollectionId	targetInstitutionCode	targetTaxonId	targetTaxonName	targetTaxonRank	targetTaxonPathIds	targetTaxonPath	targetTaxonPathNames	targetBodyPartId	targetBodyPartName	targetLifeStageId	targetLifeStageName	targetSexId	targetSexName	basisOfRecordIdbasisOfRecordName	http://rs.tdwg.org/dwc/terms/eventDate	decimalLatitudedecimalLongitude	localityId	localityName	referenceDoi	referenceUrl	referenceCitation	namespace	citation	archiveURI	lastSeenAt	contentHash	eltonVersion
listing interactions [local]... failed.
java.lang.RuntimeException: listing interactions failed.
	at org.globalbioticinteractions.elton.cmd.CmdUtil.handleNamespaces(CmdUtil.java:87)
	at org.globalbioticinteractions.elton.cmd.CmdInteractions.run(CmdInteractions.java:195)
	at org.globalbioticinteractions.elton.cmd.CmdInteractions.run(CmdInteractions.java:180)
	at org.globalbioticinteractions.elton.cmd.CmdLine.run(CmdLine.java:18)
	at org.globalbioticinteractions.elton.cmd.CmdLine.run(CmdLine.java:27)
	at org.globalbioticinteractions.elton.Elton.main(Elton.java:20)
Caused by: org.globalbioticinteractions.dataset.DatasetFinderException: failed to import datasets [local], please check the logs.
	at org.globalbioticinteractions.elton.cmd.CmdUtil.handleNamespaces(CmdUtil.java:83)
	... 5 more

expected was that the elton interactions command produced the same results no matter how often it is executed. Probably introduced by recently introduce feature #29 .

in review, include a list of verbatim interactions and their (un)interpreted counterparts.

in a elton review, we'd like to have a way to create an exhaustive list of all district verbatim interaction terms and their (un)interpreted counterparts.

e.g.,

hostof -> host of, RO_123456
eats bananas -> [blank] (not yet interpreted)

open review samples directly in a collaborative speadsheet

To make it easier look / view review or indexed-interactions, we'd like to open the review and indexed-interactions directly in a collaborative spreadsheet platform like ethercalc.org or googlesheets etc.

As a button: open in googlesheets / ethercalc

Count of records comment for report

A comment should be added to the first part of a report to clarify what is being reported. So for:

#records namespace institutionCode collectionCode interactionTypeId interactionTypeName
67819 globalbioticinteractions/ummzi UMMZ ummzi http://purl.obolibrary.org/obo/RO_0002454 hasHost

Example comment:
Count of records coming from a specific data source or "namespace" (e.g., https://github.com/globalbioticinteractions/ummzi or https://github.com/globalbioticinteractions/scan ) grouped by institutionCode, collectionCode, interactionTypeId and interactionTypeName

Reports divided by collection, not IPT/DwC

As a collection manager, I would like to see a report specifically for my collection/s. Not for all of SCAN or Vertnet (for example).

millerse/Weidinger-et-al.-2009 https://zenodo.org/record/258188 part of GloBI community but github is selected

from elton log -

millerse/Weidinger-et-al.-2009  https://zenodo.org/record/258188/files/millerse/Weidinger-et-al.-2009-v1.0.zip  f5a63d4c2f2f0407c5b932c5a6bc7238f8b784294c37ced0a60
03ad064828332        2017-09-25T23:13:21Z    
millerse/Weidinger-et-al.-2009  jar:file:/home/jhpoelen/elton/./datasets/millerse/Weidinger-et-al.-2009/f5a63d4c2f2f0407c5b932c5a6bc7238f8b784294c37ced0a6003ad0648
28332!/millerse-Weidinger-et-al.-2009-fb4eb83/interactions.tsv       5309b32d582069e06e0046ff5647128ea761c1b98db9610b3e322138055834cb        2017-09-25T23:13:21Z
    
millerse/Weidinger-et-al.-2009  https://github.com/millerse/Weidinger-et-al.-2009/archive/053eaa6ea8389419b913b1eae7ed7fed24a7b21e.zip          2017-10-02T05:24:09Z    application/globi
millerse/Weidinger-et-al.-2009  https://github.com/millerse/Weidinger-et-al.-2009/archive/053eaa6ea8389419b913b1eae7ed7fed24a7b21e.zip  1e2fa95e969f6cfa8722439fc9b1b3ed7f472ff1244a6c796209b0756feaabef        2017-10-02T05:24:09Z    
millerse/Weidinger-et-al.-2009  jar:file:/home/jhpoelen/elton/./datasets/millerse/Weidinger-et-al.-2009/1e2fa95e969f6cfa8722439fc9b1b3ed7f472ff1244a6c796209b0756feaabef!/Weidinger-et-al.-2009-053eaa6ea8389419b913b1eae7ed7fed24a7b21e/globi.json     ba2567b98019d71bc6e5aae260b9c93fbf8c8558b3e4b3ade684bdeaae0e4ccd        2017-10-02T05:24:09Z    
millerse/Weidinger-et-al.-2009  https://github.com/millerse/Weidinger-et-al.-2009/archive/053eaa6ea8389419b913b1eae7ed7fed24a7b21e.zip  1e2fa95e969f6cfa8722439fc9b1b3ed7f472ff1244a6c796209b0756feaabef        2017-10-02T05:24:10Z 

make it easier to attribute authors by their ORCID

as suggested by @tkuhn in context of http://nanopub.org

include original data that was used to populate the parsed interaction data

GloBI parses versioned original datasets into a common model. Currently, there's no explicit link between the original raw data and their parsed counterparts. However, there is an explicit link with the version of the dataset used to access the data.

Once the original data is available, we can include this in the "dataContext" of the data review.

E.g.,

"sourceDataHeader": "1.collectionobject.catalogNumber,\"1,7.accession.accessionNumber\",1.collectionobject.altCatalogNumber,1.collectionobject.catalogedDate,"1,5-cataloger.collectionobject.cataloger","1,9-determinations,4.taxon.Class","1,9-determinations,4.taxon.Subclass","1,9-determinations,4.taxon.Superorder","1,9-determinations,4.taxon.Order","1,9-determinations,4.taxon.Suborder","1,9-determinations,4.taxon.Infraorder","1,9-determinations,4.taxon.Parvorder","1,9-determinations,4.taxon.Superfamily","1,9-determinations,4.taxon.Family","1,9-determinations,4.taxon.Subfamily","1,9-determinations,4.taxon.Genus","1,9-determinations,4.taxon.Subgenus","1,9-determinations,4.taxon.Species","1,9-determinations,4.taxon.Subspecies","1,9-determinations,5-determiner.determination.determiner","1,9-determinations.determination.determinedDate","1,9-determinations.determination.typeStatusName","1,93.collectionobjectattribute.text4","1,93.collectionobjectattribute.text1","1,93.collectionobjectattribute.text8","1,10.collectingevent.startDate","1,10.collectingevent.endDate","1,10.collectingevent.verbatimDate","1,10,2.collectingevent.locality","1,10.collectingevent.stationFieldNumber","1,10.collectingevent.remarks","1,10.collectingevent.method","1,10,30-collectors.collectingevent.collectors","1,93.collectionobjectattribute.text10","1,93.collectionobjectattribute.text11","1,93.collectionobjectattribute.text12","1,93.collectionobjectattribute.text13","1,93.collectionobjectattribute.text14","1,93.collectionobjectattribute.text15","1,93.collectionobjectattribute.text16","1,93.collectionobjectattribute.text9","1,93.collectionobjectattribute.text17","1,93.collectionobjectattribute.remarks","1,63-preparations,65.preparation.prepType","1,63-preparations.preparation.countAmt",1.collectionobject.guid",
"sourceData": ",,,2016-06-01,Danielle Tanzer,Insecta,,,Odonata,ZYGOPTERA,,,,Coenagrionidae,,Argia ,,plana,,,,,adult,M,,,,07/08/1931,\"United States, Arizona, Cochise Co.; Huachuca Mts., Ramsey Canyon; 31.4587300000; -110.2968700000\",,,,\"Gloyd, Leonora\",,,,,,,,,,,Paper Triangle,1,dee674d7-219f-4f81-96a1-5dba4ee1726a"

Also include the mapping schema that translates the source data into the GloBI model (e.g., mapping columns into "GloBI" columns), in addition to the value translations made / introduced by GloBI (translating values into values that GloBI understands (e.g., "host of" -> "RO:123455").

elton update stalls due to unavailable resource dependency

The automated GloBI review of https://github.com/GoMexSI/interaction-data timed and cause an error:

https://travis-ci.org/github/GoMexSI/interaction-data/builds/728064003

   _____ _       ____ _____   _____            _                
  / ____| |     |  _ \_   _| |  __ \          (_)               
 | |  __| | ___ | |_) || |   | |__) |_____   ___  _____      __ 
 | | |_ | |/ _ \|  _ < | |   |  _  // _ \ \ / / |/ _ \ \ /\ / / 
 | |__| | | (_) | |_) || |_  | | \ \  __/\ V /| |  __/\ V  V /  
  \_____|_|\___/|____/_____| |_|  \_\___| \_/ |_|\___| \_/\_/   

 | |           |  ____| | |                                     
 | |__  _   _  | |__  | | |_ ___  _ __                          
 | '_ \| | | | |  __| | | __/ _ \| '_ \                         
 | |_) | |_| | | |____| | || (_) | | | |                        
 |_.__/ \__, | |______|_|\__\___/|_| |_|                        
         __/ |                                                  
        |___/                                                   

Reviewing [https://raw.githubusercontent.com/GoMexSI/interaction-data/master] using Elton version [0.10.2].
updating [local]... 
No output has been received in the last 10m0s, this potentially indicates a stalled build or something wrong with the build itself.
Check the details on how to adjust your build configuration on: https://docs.travis-ci.com/user/common-build-problems/#build-times-out-because-no-output-was-received

The build has been terminated

The root cause of this was that an underlying online resource (i.e. https://cmecscatalog.org/cmecs/documents/cmecs4.accdb) was no longer available.

Expected: elton stop attempting to retrieve the resource after a while (60s?), and provides error messages.

Actually: elton block on attempting to retrieve a resource.

tsv/csv report change order of columns for interactions.tsv

Put columns:

sourceTaxonId | sourceTaxonName | interactionTypeId | interactionTypeName | targetTaxonId | targetTaxonName | catalogNumber

In a row and up front. I want to see these all together without scrolling around my spreadsheet.

in [elton review] default interactionType is not applied on missing interactionType

related to ParasiteTracker/tpt-reporting#14 .

When running elton review with a record in a DwC that has associated taxa, but no defined species interaction, a review info note with message "no interaction type defined".

Expected: verbatim interaction type is "null", but interaction type contains the default interaction type (i.e., interactsWith).

Actual: verbatim interaction type is "null" and interaction type is "null".

Note that when running elton interactions, the expected default interaction type appears.

$ elton review globalbioticinteractions/ucsb-izc | grep ff61e265-5e5a-42ae-bda5-2f9c8539b2a8
creating review [globalbioticinteractions/ucsb-izc]... 
4f839752-c343-4642-b28a-a079a53888b3	2020-04-29T17:21:20Z	GloBI automated reviewer (elton-0.9.5)	globalbioticinteractions/ucsb-izc	info	biotic interaction found	https://github.com/globalbioticinteractions/ucsb-izc/archive/01ebc8d7b4d42a7ad5897f531fb6978b1b10220e.zip	https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid=123141	UCSB	IZC	e7c51ab1-870b-4ee8-9d62-092875ffa870	UCSB-IZC00024782	ff61e265-5e5a-42ae-bda5-2f9c8539b2a8	University of California Santa Barbara Invertebrate Zoology Collection. Accessed at <https://symbiota.ccber.ucsb.edu:443/content/dwca/UCSB-IZC_DwC-A.zip> on 29 Apr 2020.	{"reviewId":"4f839752-c343-4642-b28a-a079a53888b3","reviewDate":"2020-04-29T17:21:20Z","reviewerName":"GloBI automated reviewer (elton-0.9.5)","reviewCommentType":"info","reviewComment":"biotic interaction found","namespace":"globalbioticinteractions/ucsb-izc","context":{"archiveURI":"https://github.com/globalbioticinteractions/ucsb-izc/archive/01ebc8d7b4d42a7ad5897f531fb6978b1b10220e.zip","basisOfRecordName":"PreservedSpecimen","contentHash":"1f4097c2e3854d737f682c211db2a19916d5a618f82ce3cac89418571cb062e1","decimalLatitude":"34.408026","decimalLongitude":"-119.848802","http://portal.idigbio.org/terms/recordId":"urn:uuid:ff61e265-5e5a-42ae-bda5-2f9c8539b2a8","http://purl.org/dc/elements/1.1/rights":"http://creativecommons.org/publicdomain/zero/1.0/","http://purl.org/dc/terms/accessRights":"https://creativecommons.org/publicdomain/","http://purl.org/dc/terms/language":null,"http://purl.org/dc/terms/modified":"2020-02-07 09:32:05","http://purl.org/dc/terms/references":"https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid=123141","http://purl.org/dc/terms/rightsHolder":"University of California, Santa Barbara","http://rs.tdwg.org/dwc/terms/associatedTaxa":"Lupinus bicolor","http://rs.tdwg.org/dwc/terms/basisOfRecord":"PreservedSpecimen","http://rs.tdwg.org/dwc/terms/catalogNumber":"UCSB-IZC00024782","http://rs.tdwg.org/dwc/terms/class":"Insecta","http://rs.tdwg.org/dwc/terms/collectionCode":"IZC","http://rs.tdwg.org/dwc/terms/collectionID":"e7c51ab1-870b-4ee8-9d62-092875ffa870","http://rs.tdwg.org/dwc/terms/coordinateUncertaintyInMeters":null,"http://rs.tdwg.org/dwc/terms/country":"United States","http://rs.tdwg.org/dwc/terms/county":"Santa Barbara","http://rs.tdwg.org/dwc/terms/dataGeneralizations":null,"http://rs.tdwg.org/dwc/terms/dateIdentified":"2017","http://rs.tdwg.org/dwc/terms/day":"21","http://rs.tdwg.org/dwc/terms/decimalLatitude":"34.408026","http://rs.tdwg.org/dwc/terms/decimalLongitude":"-119.848802","http://rs.tdwg.org/dwc/terms/disposition":null,"http://rs.tdwg.org/dwc/terms/dynamicProperties":"associatedReferences=https://doi.org/10.1111/een.12721; associatedReferences=https://escholarship.org/uc/item/64c550mk","http://rs.tdwg.org/dwc/terms/endDayOfYear":null,"http://rs.tdwg.org/dwc/terms/establishmentMeans":null,"http://rs.tdwg.org/dwc/terms/eventDate":"2017-04-21","http://rs.tdwg.org/dwc/terms/family":"Cicadellidae","http://rs.tdwg.org/dwc/terms/fieldNumber":"LIN44","http://rs.tdwg.org/dwc/terms/genus":null,"http://rs.tdwg.org/dwc/terms/geodeticDatum":"WGS84","http://rs.tdwg.org/dwc/terms/georeferenceProtocol":null,"http://rs.tdwg.org/dwc/terms/georeferenceRemarks":null,"http://rs.tdwg.org/dwc/terms/georeferenceSources":null,"http://rs.tdwg.org/dwc/terms/georeferenceVerificationStatus":null,"http://rs.tdwg.org/dwc/terms/georeferencedBy":null,"http://rs.tdwg.org/dwc/terms/habitat":null,"http://rs.tdwg.org/dwc/terms/identificationQualifier":null,"http://rs.tdwg.org/dwc/terms/identificationReferences":null,"http://rs.tdwg.org/dwc/terms/identificationRemarks":null,"http://rs.tdwg.org/dwc/terms/identifiedBy":"J. Luong","http://rs.tdwg.org/dwc/terms/individualCount":"1","http://rs.tdwg.org/dwc/terms/informationWithheld":null,"http://rs.tdwg.org/dwc/terms/infraspecificEpithet":null,"http://rs.tdwg.org/dwc/terms/institutionCode":"UCSB","http://rs.tdwg.org/dwc/terms/kingdom":"Animalia","http://rs.tdwg.org/dwc/terms/lifeStage":null,"http://rs.tdwg.org/dwc/terms/locality":"UCSB Lagoon Island, 2016 burn plot","http://rs.tdwg.org/dwc/terms/locationRemarks":null,"http://rs.tdwg.org/dwc/terms/maximumDepthInMeters":null,"http://rs.tdwg.org/dwc/terms/maximumElevationInMeters":null,"http://rs.tdwg.org/dwc/terms/minimumDepthInMeters":null,"http://rs.tdwg.org/dwc/terms/minimumElevationInMeters":null,"http://rs.tdwg.org/dwc/terms/month":"4","http://rs.tdwg.org/dwc/terms/municipality":null,"http://rs.tdwg.org/dwc/terms/occurrenceID":"ff61e265-5e5a-42ae-bda5-2f9c8539b2a8","http://rs.tdwg.org/dwc/terms/occurrenceRemarks":"Lupinus bicolor arthropod restored vs non-restored project comparison","http://rs.tdwg.org/dwc/terms/order":"Hemiptera","http://rs.tdwg.org/dwc/terms/otherCatalogNumbers":null,"http://rs.tdwg.org/dwc/terms/ownerInstitutionCode":null,"http://rs.tdwg.org/dwc/terms/phylum":"Arthropoda","http://rs.tdwg.org/dwc/terms/preparations":"Pinned","http://rs.tdwg.org/dwc/terms/recordNumber":null,"http://rs.tdwg.org/dwc/terms/recordedBy":"Justin Luong","http://rs.tdwg.org/dwc/terms/reproductiveCondition":null,"http://rs.tdwg.org/dwc/terms/samplingEffort":null,"http://rs.tdwg.org/dwc/terms/samplingProtocol":"Caught with Net","http://rs.tdwg.org/dwc/terms/scientificName":"Cicadellidae","http://rs.tdwg.org/dwc/terms/scientificNameAuthorship":null,"http://rs.tdwg.org/dwc/terms/sex":null,"http://rs.tdwg.org/dwc/terms/specificEpithet":null,"http://rs.tdwg.org/dwc/terms/startDayOfYear":"111","http://rs.tdwg.org/dwc/terms/stateProvince":"California","http://rs.tdwg.org/dwc/terms/taxonID":"3594","http://rs.tdwg.org/dwc/terms/taxonRank":null,"http://rs.tdwg.org/dwc/terms/taxonRemarks":null,"http://rs.tdwg.org/dwc/terms/typeStatus":null,"http://rs.tdwg.org/dwc/terms/verbatimCoordinates":null,"http://rs.tdwg.org/dwc/terms/verbatimDepth":null,"http://rs.tdwg.org/dwc/terms/verbatimElevation":null,"http://rs.tdwg.org/dwc/terms/verbatimEventDate":"April 21, 2017","http://rs.tdwg.org/dwc/terms/year":"2017","http://symbiota.org/terms/recordEnteredBy":"hayleerosso","interactionTypeId":"http://purl.obolibrary.org/obo/RO_0002437","interactionTypeName":"interactsWith","interactionTypeNameVerbatim":"associated with","localityName":"UCSB Lagoon Island, 2016 burn plot","referenceCitation":"https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid=123141","referenceUrl":"https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid=123141","sourceCatalogNumber":"UCSB-IZC00024782","sourceCollectionCode":"IZC","sourceCollectionId":"e7c51ab1-870b-4ee8-9d62-092875ffa870","sourceInstitutionCode":"UCSB","sourceOccurrenceId":"ff61e265-5e5a-42ae-bda5-2f9c8539b2a8","sourceTaxonClass":"Insecta","sourceTaxonFamily":"Cicadellidae","sourceTaxonKingdom":"Animalia","sourceTaxonName":"Cicadellidae","sourceTaxonOrder":"Hemiptera","sourceTaxonPath":"Animalia | Arthropoda | Insecta | Hemiptera | Cicadellidae","sourceTaxonPathNames":"kingdom | phylum | class | order | family","sourceTaxonPhylum":"Arthropoda","studySourceCitation":"University of California Santa Barbara Invertebrate Zoology Collection. Accessed at <https://symbiota.ccber.ucsb.edu:443/content/dwca/UCSB-IZC_DwC-A.zip> on 29 Apr 2020.","studyTitle":"https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid=123141","targetTaxonName":"Lupinus bicolor"}}
4f839752-c343-4642-b28a-a079a53888b3	2020-04-29T17:21:20Z	GloBI automated reviewer (elton-0.9.5)	globalbioticinteractions/ucsb-izc	info	no interaction type defined		https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid=123141	UCSB	IZC	e7c51ab1-870b-4ee8-9d62-092875ffa870	UCSB-IZC00024782	ff61e265-5e5a-42ae-bda5-2f9c8539b2a8		{"reviewId":"4f839752-c343-4642-b28a-a079a53888b3","reviewDate":"2020-04-29T17:21:20Z","reviewerName":"GloBI automated reviewer (elton-0.9.5)","reviewCommentType":"info","reviewComment":"no interaction type defined","namespace":"globalbioticinteractions/ucsb-izc","context":{"sourceCollectionCode":"IZC","http://rs.tdwg.org/dwc/terms/maximumElevationInMeters":null,"http://rs.tdwg.org/dwc/terms/preparations":"Pinned","sourceTaxonClass":"Insecta","http://rs.tdwg.org/dwc/terms/infraspecificEpithet":null,"http://rs.tdwg.org/dwc/terms/habitat":null,"http://rs.tdwg.org/dwc/terms/otherCatalogNumbers":null,"http://rs.tdwg.org/dwc/terms/taxonRank":null,"decimalLatitude":"34.408026","http://rs.tdwg.org/dwc/terms/year":"2017","http://rs.tdwg.org/dwc/terms/lifeStage":null,"http://rs.tdwg.org/dwc/terms/identificationQualifier":null,"localityName":"UCSB Lagoon Island, 2016 burn plot","http://rs.tdwg.org/dwc/terms/typeStatus":null,"http://rs.tdwg.org/dwc/terms/ownerInstitutionCode":null,"http://purl.org/dc/elements/1.1/rights":"http://creativecommons.org/publicdomain/zero/1.0/","http://rs.tdwg.org/dwc/terms/locationRemarks":null,"studyTitle":"https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid=123141","http://rs.tdwg.org/dwc/terms/specificEpithet":null,"http://rs.tdwg.org/dwc/terms/occurrenceID":"ff61e265-5e5a-42ae-bda5-2f9c8539b2a8","http://rs.tdwg.org/dwc/terms/samplingProtocol":"Caught with Net","http://rs.tdwg.org/dwc/terms/informationWithheld":null,"basisOfRecordName":"PreservedSpecimen","referenceUrl":"https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid=123141","http://rs.tdwg.org/dwc/terms/georeferenceSources":null,"http://rs.tdwg.org/dwc/terms/identificationReferences":null,"sourceTaxonPathNames":"kingdom | phylum | class | order | family","http://rs.tdwg.org/dwc/terms/establishmentMeans":null,"http://rs.tdwg.org/dwc/terms/decimalLongitude":"-119.848802","http://rs.tdwg.org/dwc/terms/dataGeneralizations":null,"http://rs.tdwg.org/dwc/terms/startDayOfYear":"111","http://rs.tdwg.org/dwc/terms/georeferenceProtocol":null,"sourceCollectionId":"e7c51ab1-870b-4ee8-9d62-092875ffa870","http://rs.tdwg.org/dwc/terms/taxonID":"3594","referenceCitation":"https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid=123141","sourceTaxonPath":"Animalia | Arthropoda | Insecta | Hemiptera | Cicadellidae","http://rs.tdwg.org/dwc/terms/georeferenceVerificationStatus":null,"http://rs.tdwg.org/dwc/terms/taxonRemarks":null,"http://purl.org/dc/terms/rightsHolder":"University of California, Santa Barbara","http://rs.tdwg.org/dwc/terms/samplingEffort":null,"http://purl.org/dc/terms/modified":"2020-02-07 09:32:05","http://rs.tdwg.org/dwc/terms/decimalLatitude":"34.408026","http://rs.tdwg.org/dwc/terms/recordedBy":"Justin Luong","sourceTaxonPhylum":"Arthropoda","http://rs.tdwg.org/dwc/terms/kingdom":"Animalia","http://rs.tdwg.org/dwc/terms/county":"Santa Barbara","http://rs.tdwg.org/dwc/terms/minimumDepthInMeters":null,"http://rs.tdwg.org/dwc/terms/class":"Insecta","sourceTaxonFamily":"Cicadellidae","http://purl.org/dc/terms/language":null,"http://rs.tdwg.org/dwc/terms/dynamicProperties":"associatedReferences=https://doi.org/10.1111/een.12721; associatedReferences=https://escholarship.org/uc/item/64c550mk","http://rs.tdwg.org/dwc/terms/individualCount":"1","http://rs.tdwg.org/dwc/terms/georeferenceRemarks":null,"sourceTaxonKingdom":"Animalia","http://rs.tdwg.org/dwc/terms/eventDate":"2017-04-21","http://purl.org/dc/terms/references":"https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid=123141","http://rs.tdwg.org/dwc/terms/institutionCode":"UCSB","http://rs.tdwg.org/dwc/terms/disposition":null,"http://rs.tdwg.org/dwc/terms/fieldNumber":"LIN44","http://rs.tdwg.org/dwc/terms/verbatimEventDate":"April 21, 2017","http://rs.tdwg.org/dwc/terms/country":"United States","associatedReferences":"https://escholarship.org/uc/item/64c550mk","http://rs.tdwg.org/dwc/terms/order":"Hemiptera","http://rs.tdwg.org/dwc/terms/minimumElevationInMeters":null,"http://purl.org/dc/terms/accessRights":"https://creativecommons.org/publicdomain/","http://rs.tdwg.org/dwc/terms/locality":"UCSB Lagoon Island, 2016 burn plot","http://rs.tdwg.org/dwc/terms/endDayOfYear":null,"http://rs.tdwg.org/dwc/terms/basisOfRecord":"PreservedSpecimen","http://rs.tdwg.org/dwc/terms/verbatimDepth":null,"http://rs.tdwg.org/dwc/terms/stateProvince":"California","http://rs.tdwg.org/dwc/terms/scientificName":"Cicadellidae","http://rs.tdwg.org/dwc/terms/day":"21","http://rs.tdwg.org/dwc/terms/collectionID":"e7c51ab1-870b-4ee8-9d62-092875ffa870","http://rs.tdwg.org/dwc/terms/genus":null,"decimalLongitude":"-119.848802","http://rs.tdwg.org/dwc/terms/georeferencedBy":null,"http://rs.tdwg.org/dwc/terms/occurrenceRemarks":"Lupinus bicolor arthropod restored vs non-restored project comparison","http://rs.tdwg.org/dwc/terms/reproductiveCondition":null,"http://symbiota.org/terms/recordEnteredBy":"hayleerosso","http://rs.tdwg.org/dwc/terms/verbatimCoordinates":null,"sourceInstitutionCode":"UCSB","http://portal.idigbio.org/terms/recordId":"urn:uuid:ff61e265-5e5a-42ae-bda5-2f9c8539b2a8","http://rs.tdwg.org/dwc/terms/collectionCode":"IZC","http://rs.tdwg.org/dwc/terms/municipality":null,"sourceCatalogNumber":"UCSB-IZC00024782","http://rs.tdwg.org/dwc/terms/recordNumber":null,"http://rs.tdwg.org/dwc/terms/sex":null,"http://rs.tdwg.org/dwc/terms/family":"Cicadellidae","http://rs.tdwg.org/dwc/terms/month":"4","sourceOccurrenceId":"ff61e265-5e5a-42ae-bda5-2f9c8539b2a8","http://rs.tdwg.org/dwc/terms/phylum":"Arthropoda","http://rs.tdwg.org/dwc/terms/coordinateUncertaintyInMeters":null,"sourceTaxonOrder":"Hemiptera","sourceTaxonName":"Cicadellidae","http://rs.tdwg.org/dwc/terms/verbatimElevation":null,"http://rs.tdwg.org/dwc/terms/associatedTaxa":"Lupinus bicolor","http://rs.tdwg.org/dwc/terms/identifiedBy":"J. Luong","http://rs.tdwg.org/dwc/terms/scientificNameAuthorship":null,"http://rs.tdwg.org/dwc/terms/catalogNumber":"UCSB-IZC00024782","http://rs.tdwg.org/dwc/terms/maximumDepthInMeters":null,"http://rs.tdwg.org/dwc/terms/geodeticDatum":"WGS84","http://rs.tdwg.org/dwc/terms/dateIdentified":"2017","http://rs.tdwg.org/dwc/terms/identificationRemarks":null,"targetTaxonName":null}}
done.
$ elton interactions globalbioticinteractions/ucsb-izc | grep ff61e265-5e5a-42ae-bda5-2f9c8539b2a8
listing interactions [globalbioticinteractions/ucsb-izc]... 
https://en.wiktionary.org/wiki/support	ff61e265-5e5a-42ae-bda5-2f9c8539b2a8	UCSB-IZC00024782	IZC	e7c51ab1-870b-4ee8-9d62-092875ffa870	UCSB		Cicadellidae		Animalia | Arthropoda | Insecta | Hemiptera | Cicadellidae	kingdom | phylum | class | order | family			http://purl.obolibrary.org/obo/RO_0002437	interactsWith							Lupinus bicolor												PreservedSpecimen	2017-04-21T00:00:00Z	34.408026	-119.848802		UCSB Lagoon Island, 2016 burn plot		https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid=123141	https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid=123141	globalbioticinteractions/ucsb-izc	University of California Santa Barbara Invertebrate Zoology Collection	https://github.com/globalbioticinteractions/ucsb-izc/archive/01ebc8d7b4d42a7ad5897f531fb6978b1b10220e.zip	2020-04-29T00:49:27.387Z	1f4097c2e3854d737f682c211db2a19916d5a618f82ce3cac89418571cb062e1	0.9.5
done.

include interaction records without review comments in elton review report

@neilcobb expressed a desire to get a list of records that were reviewed using elton check and did not generate any review comments.

Suggest to include a reviewComment type (e.g., informational, warning, etc) to allow for including "passed review" messages into review reports.

tsv/csv reports: rename review-note

rename review-note to indicate its a list of possible errors. name it as review-issues, or records-for-review

0.12.1 not 0.12.2

When I updated elton it suggests it is version 0.12.1. The latest release is said to be 0.12.2

Thanks!

tsv/csv report Names.tsv

Include how it is mapped to the taxonomy in GloBI? Iist of name ids (TTD:0000123, GBIF:2827749, etc.)