echinopscis / echinopscis-sample-vault Goto Github PK

This because echinopscis-quickadd was deprectaed and all scripts moved to be managed inside this echinopscis-sample-vault repo.

The grscicoll search is currently constrained to Index Herbariorum (IH) records only. IH contains lat/long for institutions so grscicoll collection pages could include location coordinates and therefore be plottable on a map.
The grscicoll script would need to:

• Retrieve coordinates
• Write coordinates into frontmatter as a "location" entry

Obsidian can manage PDFs as attachments, displaying them inline.

The "start here" demonstration could show this functionality, so a folder structure in which to store these would be useful too.

• Add content to Start here.md
• Add folder by creating .gitkeep placeholder under remote-data\pdfs
• Add icon to folder by selecting remix icon, saving svg representation to: .obsidian/plugins/obsidian-icon-folder/icons/myicons

The IPNI script supports an "Retrieve linked names" option and if the selected name is a combination, the basionym is also retrieved and saved.
This function should also work from basionym to combination(s) - ie if a basionym is selected, the combinations of that name (there may be more than one) should also be added.

Several installation options:

• Github gist with JavaScript snippet: https://gist.github.com/kepano/90c05f162c37cf730abb8ff027987ca3
• Chrome extension: https://chrome.google.com/webstore/detail/obsidian-clipper/mphkdfmipddgfobjhphabphmpdckgfhb?hl=en
• Firefox extension: https://addons.mozilla.org/en-GB/firefox/addon/obsidian-web-clipper/

Provides definitions for technical terms

makes folder view more usable by indicating type of content held in remote folders

Requirement for filtering in leaflet maps

If a user clips semi-structured text from a journal article into Obsidian, the scientific names may be presented with abbreviated genus names, as the context is determined from the containing paper.

The IPNI name search script could do the following:

• Read the frontmatter, and look for a "genus_context" entry
• If the search string starts with the first letter of the genus_context entry followed by '. ' then replace it before doing the IPNI name search.

This would ensure that paragraphs like the following could easily be searched by highlighting the species names, even if they are abbreviated (currently only the first could be searched by highlighting the existing text):

These new species are all relatively rare, but not currently of conservation concern. Solanum aspersum sp. nov. is distributed in Colombia and Ecuador, S. luculentum sp. nov. in Colombia and Venezuela, S. sanchez-vegae sp. nov. is endemic to northern Peru and S. sousae sp. nov. to southern Mexico. Solanum luculentum has the morphology of a dioecious species; this is the first report of this breeding system in the Dulcamaroid clade.

The script would receive "S. luculentum" (from document.getSelection()), check the frontmatter (app.metadataCache.getFileCache(file).frontmatter) for a genus_context entry, replace "S." with "Solanum" and proceed with the search and display of matches. If no genus context is available or if the abbreviation does not match then the search should proceed as normal.

The IPNI quickadd script can be configured to retrieve related records (eg also retrieve the basionym if the selected record is a combination). It would be useful to allow the GBIF occurrence quickadd script to optionally retrieve clustered occurrences.

eg:

QuickAdd:IPNI -> QuickAdd: Scientific names (IPNI)
QuickAdd:GBIF -> QuickAdd: Specimen occurrences (GBIF)
QuickAdd:Bionomia -> QuickAdd: Collector / determiner profiles (Bionomia)
QuickAdd: GRSciColl -> QuickAdd:Collection profiles (Index Herbariorum via GRSciColl)

This sample vault holds the scripts and templates from echinopscis/echinopscis-quickadd. Instead of replicating the scripts here, it would be better to have a github actions build process that pulls the quickadd scripts and implements the default configuration in quickadd by manipulating .obsidian/plugins/quickadd/data.json

IPNI citation data includes DOI, so this can be used to search crossref and establish a literature note when the name is added (if the relevant literature note is not already in the vault)