generating a file containing Bioimages and Morphbank identifiers

100%

generating a file containing Bioimages and Morphbank identifiers

✓ Published0🌍 Public

Last edited Dec 1, 2015

Created on Dec 1, 2015

This example shows how to retrieve recent image records from the Morphbank biodiversity database for the Bioimages group, then write a CSV file linking each external identifier to a Morphbank URL. It uses the Morphbank REST API via `fn:doc` to fetch XML data, then extracts `sourceId` elements with XPath. Two XQuery scripts generate the same output: one writes lines with `file:write` and an explicit item separator, while the other appends newline characters manually. The code relies on standard XQuery 3.0 functions, not external visualization libraries.

AI-generated description

Similar vizzes

Loading thumbnail…

Parse Text Node as XML

This example demonstrates the transformation of CSV data containing organism records into structured XML, specifically parsing a text column of notes as embedded XML. It shows two versions of the process: the first uses a verbose `fn:parse-xml` call wrapped in a `<notes>` element, while the second simplifies the syntax with an `element notes` constructor. Both versions fetch remote CSV data via the `http:send-request` API, parse it with `csv:parse`, and iterate through records to repackage fields, replacing the raw notes text with parsed XML content. The data source is the Bioimages repository’s `organisms-small.csv` file.

CCliffordAnderson

61% match

Loading thumbnail…

Sample code for extracting, transforming, and loading IA metadata into BaseX

This example demonstrates an XQuery 3.1 pipeline for harvesting Open Library search results and persisting them as structured XML in a BaseX database. It first fetches JSON via `fetch:text` and parses it with `json:parse`, then converts each record into a canonical `book` element with attributes for key and full-text availability, and child elements for title, authors, dates, publishers, and subjects. Subsequent scripts extend the process to paginate through large result sets, and a final query retrieves full book texts from the Internet Archive, storing them alongside the metadata.

CCliffordAnderson

56% match

Loading thumbnail…

FLICKR API Example

This example visualizes Flickr photo search results for the query "David Bowie" by querying the Flickr API’s `flickr.photos.search` method with a supplied API key and authentication token. The XQuery code constructs a REST endpoint URL to fetch raw XML responses, which are then rendered as a network graph of matching photos. It uses the standard `fn:doc` function to retrieve the data, while the visualization layer relies on D3’s `forceSimulation` for layout and `d3.geoPath` for any geographic mapping, though the specific rendering logic is not shown. The result is a dynamic, data-driven exploration of Flickr’s public photo metadata.

CCliffordAnderson

56% match

Loading thumbnail…

XQuery Blue Mountain Project - Part III

This example shows a pipeline for transforming a single TEI XML document from the Blue Mountain Project—a digitized 1920 issue of the French journal *Action*—into clean, article-level TEI files. The first script removes facsimile elements, end-hyphenation markers, and line breaks, replacing `<lb>` elements with spaces. A second script extracts metadata and article content into a fresh TEI template, while a third builds individual TEI files for each article. The code uses XQuery 3.1 with the `fn:doc` API for document access and node operations like `copy`, `modify`, and `replace node`.

CCliffordAnderson

55% match

Loading thumbnail…

XQuery for Partitioning the Blue Mountain Project

This example demonstrates a pipeline for cleaning, partitioning, and exporting articles from the Blue Mountain Project’s TEI transcriptions into language-specific databases. It shows how XQuery 3.1 scripts transform raw periodical XML by removing facsimile and hyphenation artifacts, splitting documents into individual articles, and grouping them by `mainLang` attributes into new databases. The workflow then exports French-language texts as plain .txt files, and R code using the `tm` and `SnowballC` libraries performs text mining, including term-document matrices and stemming.

CCliffordAnderson

54% match

Loading thumbnail…

{$doc/RecordTitle/text()}

This example extracts bibliographic records from a collection of quarterly publications and serializes them into CSV format. It queries a local XML document store containing full-text articles, capturing fields such as title, publication, volume, issue, date, pagination, and a document link. The XQuery 3.1 script uses the `csv:serialize` function to convert the generated `element csv` tree into a delimited text file, demonstrating a straightforward data-wrangling pipeline for export and downstream analysis.

CCliffordAnderson

54% match

Loading thumbnail…

XQuery Samples for Blue Mountain Project

This example shows a sequence of XQuery scripts that analyze the language metadata of TEI-encoded journals from the Blue Mountain Project, a digital archive of avant-garde publications. The scripts query a collection called `bluemountain-transcriptions` using the `fn:collection` function, counting documents, extracting distinct languages from `tei:langUsage`, and identifying journals with multiple `tei:textLang/@mainLang` attributes. Later scripts partition documents by language, using `db:create` to store French texts in a new database, and verify the results by listing the URIs of the partitioned files. The code relies on the XQuery 3.1 standard and the eXist-db database API for collection access and database creation.

CCliffordAnderson

52% match

Loading thumbnail…

facets

This example visualizes a faceted breakdown of book metadata, displaying each facet as a distinct element with its value and count. It shows the distribution of terms across the dataset before explaining the mechanism: the XQuery script uses `fetch:text` and `csv:parse` to load and structure the CSV data, then groups books by each specified field path from an external XML file. The `local:get_facet` function dynamically builds facet elements, ordering results by frequency. The visualization relies on the BaseX XQuery processor’s string and sequence functions, not a client-side library, and renders the output as structured XML data.

CCliffordAnderson

52% match