TaxoDros - The Repository of the Database on Taxonomy of Drosophilidae

There is a newer version of the record available.

Published February 28, 2024 | Version v3
Dataset Open

TaxoDros - The Database on Taxonomy of Drosophilidae hash://md5/26a67012dde325cf2a3a058cc2f9c1b8 hash://sha256/ca86d74b318a334bddbc7c6a387a09530a083b8617718f5369ad548744c602d3

Creators

  • 1. Universität Zürich

Description

This repository contains the TaxoDros source data for Taxodros: The database on Taxonomy of Drosophilidae as provided by Gerhard Bächli, the database maintainer, in January 2024.

## Index Files 

filename description (click for details) signature
ALLORTE.TEXT location information hash://md5/77e26a0a38a282bb551a90e49c09693c
ASHBURN.TEXT journal names hash://md5/dfb792282c3df43a4a4d3075b126087f
DROS3.TEXT reference descriptors hash://md5/b5e2b6c6de1dc02a5c60563008a04aec
DROS5.TEXT reference details hash://md5/ff86b940567d278e50fa00672cf96629
KEYWORDS.TEXT descriptors and country names hash://md5/21884e43a0cc0728badd1b259e2f0191
README.md this file  
SPECIES-LIST_GE_SG all Drosophilid-epithets (species, infra-specific names, such as “melanogaster”), including the respective genus and subgenus name hash://md5/be40d900cf2651cb84e0c1efeca04078
SPECIES-LIST_GR_SR (species-)groups and subgroups hash://md5/0a9ebec3f9e7232de32984968323b0c2
SPECIES-LIST_GR_SR_SC (species-)group, subgroup and species-complex hash://md5/f0f08d3680b7c2aedede94af3ae17b52
SYST.QE.TEXT copy of the SYST.TEXT as a mere text-file without header hash://md5/15f77599972d23183c85228c45737e52
SYST.TEXT all systematic relationships, including synonymy hash://md5/5f4f55df4ba69a2c4c251b5c3f4166dc
TAXA_LIST all taxa (as abbreviation), for species with the currently accepted genus name, and the actual bibliographic reference hash://md5/39c8a83fb25463d18976c48d2ac0bf49


## PDF Files

TaxoDros keeps a library of associated pdfs. See [pdf](pdf/) for more information.

Details based on description provided by Bächli in January 2024.
 
The TaxoDros Index includes 12 files. With the exception of SYST.TEXT all files are strict size-limited (72 Chars, some lines with continuations in DROS5.TEXT). The font used is Monaco, a fix-length font on Mac, which in a text editor makes the data looking (pseudo)tabellaric. The following information is important to understand the individual files.
 
### ALLORTE.TEXT
 
This file includes all collection sites in alphabetical order, with geographic coordinates, first geographic longitude, then geographic latitude („-„ at the end means rather exact data) und die Swiss coordinates [This is used for Swiss Topo maps], followed by the (abbreviated) name of the country. The abbreviations are explained and expanded in KEYWORDS.TEXT and used in Taxodros online.
 
 
### ASHBURN.TEXT
 
This text-file containes the names of the journals:
*s = abbreviation of names used in DROS5.TEXT
*u = full (formal) names of journals
 
 
### DROS3.TEXT
 
This text-file includes the descriptors (keywords) used for each source. Each segment has two tags: .TEXT; and .DESC;. The tag .TEXT; includes first the source identification and may be followed by collecting localities (each beginning with =e=…). The tag .DESC; is followed by the “short name” of the taxon (always in first place) followed by the descriptors (key words), The keywords used are explained in KEYWORDS.TEXT. With the exception of the tags, all the following lines are in lower case. Addional “short names” can follow in each segment, in case that the keywords also apply. The keyword “descr” is also used in connection with the keywords fig, egg, larv, pup. Multiple segments are used for each source, when needed.
 
Example (copy of two segments in DROS3.TEXT):
 
.TEXT; tag
acurio et al., 2013 (source identification)
=e=san jose beach (collection site)
.DESC; tag
machalilla (“short name”)
descr keyword, followed by additional 
descriptors)
fig
malex
malin
femex
femin
typemat
typeloc
loc
distr$
Ecuador country of collections site
comp
affil
taxon
phyl
egg
pup
biol
.TEXT; tag
acurio et al., 2013 (source information)
.DESC; tag
atalaia-gr (“short name“)
descr (keyword)
taxaincl (keyword)
affil (keyword)
taxon (keyword)
phyl (keyword)
 
### DROS5.TEXT
 
This text-file contains segments with the bibliographic details for each source of information. Each segment begins with the tag .TEXT; strictly followed by the following tags: .A , .J , .S , .Z or .Z., .K , .P . All tags are fix length (max. 72 chars), excepting the tags .A and .S which may have consecutive lines without new tags.
 
The following is important:
 * There is only one segment for each source of information.
 * Excepting the source identification (in lowercase), all tags may contain text with the usual capitalization.
 * The lines “source identification” in DROS3.TEXT and DROS5.TEXT are in exact match, connecting the two files.
 
Explanation of the tags used within each segment:
 
.TEXT; Segment delimiter
.A source identification
.J year of publication
.S title
.Z Journal name (abbreviated), volume(issue):first 
page-last page
or
.Z. for Books: editor etc.
.K comments: library codes, pdf quality, DOI
.P name of respective pdf, if available
 
Example: (copy of segment in DROS5.TEXT)
 
.TEXT;
acurio et al., 2013
.A Acurio, A., Rafael, V., Cespedes, D., and Ruiz, A.,
.J 2013
.S Description of a New Spotted Wing Drosophila
(Diptera: Drosophilidae) Species and Its Evolutionary
Relationships Inferred by a Cladistic Analysis of
Morphological Traits.
.Z Ann. ent. Soc. Am., 106:1-11.
.K ocr++ / DOI:10.1603.AN13028
.P Acurio et al., 2013
 
### KEYWORDS.TEXT
 
This text-file includes the descriptors (keywords) used in DROS3.TEXT and the (abbreviated) names of countries used in ALLORTE.TEXT and DROS5.TEXT, all used in online TAXODROS.
 
### SPECIES-List_GE_SG
 
In this text-file, all taxon names (short names, epithets) are listed with their affiliation to genus and subgenus.
 
### SPECIES-List_GR_SG
 
In this text-file, all taxon names (short names, epithets) are listed with their affiliation to genus, subgenus, specie-groups and specie-subgroups.
 
### SPECIES-List_GR_SR_SC
 
In this text-file, all taxon names (short names, epithets) are listed with their affiliation to genus, subgenus, species-group, species-subgroup and species-complex.
 
### SYST.TEXT
 
This is a XLS-file in text/tab format. It includes all systematic relationships, including comments on synonymy and homonymy, etc., with tags for sorting. 
Some tags:
 
.KF “short name“, used in DROS3.TEXT. So called homonyms 
are separated by nummers and uniquely identified.
Additional tags refer the affiliation with family, 
subfamily, etc, where applicable.
.VN the currently accepted name (taxonomy).
.FU the original form of the name, with author(s), etc.,. 
.OR the original generic affiliation of the name
.AU the original source to link with DROS5.TEXT
 
### SYST.QE.TEXT
 
This is a text-file, actually an exact copy of the file SYST.TEXT without connection with xls.
 
### TAXA-LIST
 
This text-file lists all “short names” with actual genus affiliation and author(s) combination.
 
 
### TAXODROS
The link [https://www.taxodros.uzh.ch](https://www.taxodros.uzh.ch) allows search with keywords, search for distribution and contains lists for taxonomic overviews.

Technical info

## Provenance 

This section details the provenance of the TaxoDros index files and associated pdf files. 

### for humans

The TaxoDros index files and associated pdfs where provided by Gerhard Bächlin January 2024. Following, the index files and associated pdf files were packaged, signed, and versioned using Preston ([Elliott et al. 2020](#elliott2020), [Elliott et al. 2023](#elliott2023)).

## for machines

The information below is intended for machines to increase the machine readability of this publication. 

preston head produced the provenance anchor of this version:


hash://sha256/ca86d74b318a334bddbc7c6a387a09530a083b8617718f5369ad548744c602d3


preston\
 history\
 --anchor hash://sha256/ca86d74b318a334bddbc7c6a387a09530a083b8617718f5369ad548744c602d3
 --remote https://linker.bio,https://softwareheritage.org

yields 


<hash://sha256/ca86d74b318a334bddbc7c6a387a09530a083b8617718f5369ad548744c602d3> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/1953f4ef164ae47fb22a8ee8bba1d95fa17463a38432d4e48b9e9cf0f91dadcf> .
<hash://sha256/1953f4ef164ae47fb22a8ee8bba1d95fa17463a38432d4e48b9e9cf0f91dadcf> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/8c9cb7b31a0a5aec41be569199e3c2aa5f38fff604204914a0cae0a6239e4769> .
<hash://sha256/8c9cb7b31a0a5aec41be569199e3c2aa5f38fff604204914a0cae0a6239e4769> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/e05466f33c755f11bd1c2fa30eef2388bf24ff7989931bae1426daff0200af19> .
<hash://sha256/e05466f33c755f11bd1c2fa30eef2388bf24ff7989931bae1426daff0200af19> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/dc11cb282d103aa4541c8b406502ab5721bfc41edb662b7b44ef91a76b60dfb8> .
<hash://sha256/dc11cb282d103aa4541c8b406502ab5721bfc41edb662b7b44ef91a76b60dfb8> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/3e41eec4c91598b8a2de96e1d1ed47d271a7560eb6ef350a17bc67cc61255302> .
<hash://sha256/3e41eec4c91598b8a2de96e1d1ed47d271a7560eb6ef350a17bc67cc61255302> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://sha256/ee72b70df451082289193cdd8ff420495b3a24d230880613f9adddc71380fee6> .
<urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/ee72b70df451082289193cdd8ff420495b3a24d230880613f9adddc71380fee6> .

Similarly, in md5 hash space:

preston head --algo md5 yielded:


hash://md5/26a67012dde325cf2a3a058cc2f9c1b8

with


preston\
 history\
 --anchor hash://md5/26a67012dde325cf2a3a058cc2f9c1b8\
 --remote https://linker.bio,https://zenodo.org\
 --algo md5

produced:


<hash://md5/26a67012dde325cf2a3a058cc2f9c1b8> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://md5/40c28eb355268787eca4eba676a6fdf6> .
<hash://md5/40c28eb355268787eca4eba676a6fdf6> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://md5/3793ab3633d3e94a40d3ab442b6cff7d> .
<hash://md5/3793ab3633d3e94a40d3ab442b6cff7d> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://md5/4fa9eeed1c8cff2490483a48c718df02> .
<hash://md5/4fa9eeed1c8cff2490483a48c718df02> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://md5/b8c3a1e1acdfaf8e0bb3c69d220709d8> .
<hash://md5/b8c3a1e1acdfaf8e0bb3c69d220709d8> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://md5/d68c923002c43271cee07ba172c67b0b> .
<hash://md5/d68c923002c43271cee07ba172c67b0b> <http://www.w3.org/ns/prov#wasDerivedFrom> <hash://md5/1037a9c831005710dc9bf14ee9a2e053> .
<urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://md5/1037a9c831005710dc9bf14ee9a2e053> .

Files

README.md

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Additional details

References