Milestone 8.15: Report on existing processing services and analytical services:
An analysis of the meta-data of the services available by the major projects, initiatives, fora and
organizations
By Christos Arvanitidis, Sarah Faulwetter, Alexander Kruppa
Introduction
This field of research development is vast and fast evolving over the last couple of decades.
The scientific community has made such a progress that at the moment it is not possible to know even
the exact number of the facilities existing for the process and analysis of information and data relevant
with the disciplines of taxonomy, biogeography and ecology. For example, the search over google with
the key words “processing services”, “analytical services”, “taxonomy” brings 3,100,000 hits while it's
being reduced down to 130,000 when the additional key words “biogeography” and “ecology” are
added.
Therefore, this analysis must be restricted to a set of services available on the internet which
are manageable in terms of numbers, operational features and use. For this reason only those offered
by the mostly used sites (e.g. WoRMS, FishBase, GBIF, OBIS, uBIO, etc.) have been included in this
report.
The methodological approach followed is simple and effective. The overall objective is to
explore how (dis)similar are these services and where this (dis)similarity is coming from in terms of
operational features and functionality. In order to define an objective and reproducible approach, the
following four steps have been followed:
(a) to identify the processing and analytical tools and services offered by the sites of major projects,
initiatives, fora and organizations, such as those mentioned above;
(b) to use a set of classification identifiers, that is technical and functional features, for the adequate
characterization of their operational features and functionality (see below);
(c) to describe the processing and analytical tools available through the coding of their classification
identifiers (1,0, for presence, absence, respectively);
(d) to provide information on their relationships ((dis)similarities) through standard multivariate
analysis algorithms.
The following processing and analytical services taken into account are (full names in the
presentation section):
1. WoRMS: TaxonMatch
2. FishBase: Fish Class identification
3. FishBase: Keys of fish species identification
4. FishBase: Species Identification Using Morphometric Measurements
5. FishBase: IncoFish
6. FishBase: Aquamaps
7. GBIF: DWCA&Validator
8. GBIF: taxon tagger
9. GBIF: name finder
10. GBIF: GPAAMP
11. GBIF: BIDDSAT
12. uBIO: LinkIT
13. uBIO: FindIT
14. uBIO: Author Abbreviation Resolver
15. uBIO: TNS name mapper
16. uBIO: ParseIT
17. uBIO: CanonizeIT
18. uBIO: x:ID
19. ALA: Spatial Portal
20. OBIS: mapper
21. IBEM: ecological quality index
22. mMWeb: MAMS
23. mMWeb: CSM
24. mMWeb: ENFA.
The established categories of classification identifiers are:
Description
1. Describes data
2. Describes meta-data
3. Dynamical linking out facility with with reference systems
4. File Validating options
5. Freely distributable
6. Open source
7. Includes / applied to terrestrial species
8. Includes / applied to marine species
9. Includes / applied to fresh water species
10. Provides Literature resources
Input functions
11. Use of info and data from external resources (e.g. URL, other databases or file uploading)
12. Provides Glossary
13. Provides (bio-)Geographic area finder
14. Provides Names finder
15. Provides Authority search and match (name+year)
16. Provides Year match facility (with taxon requested)
17. Provides Extra searching facilities (row, column delimiter)
18. Provides Taxa range match facility (from to, or taxon x)
19. Interactive taxonomic key facility
20. Dichotomous/pictorial key facility
Output functions
21. Tool/service by geographic area
22. Highlighting not matched names
23. Taxonomic rank and nomenclature annotation
24. Taxon morphology info
25. Taxon morphometrics
26. Taxon photo match
27. Taxon description
28. Mapping tools (lat-long, FAO, biodiversity, etc)
29. Modeling facility on mapping (climate change, invasive species, ecological niche, etc)
30. Ecological quality indexing facility
31. Output file options facility
32. Output file as input file for other operations
Detailed presentation of the processing and analytical services
The processing and analytical services taken into account in this report are presented below in
detail. Their names, acronyms, URLs, as well as their coding according to the classification identifiers
is provided.
1. World Register of Marine Species – TaxonMatch
(http://www.marinespecies.org/aphia.php?p=match): This is a processing service which checks the
validity of any list of names of marine taxa and provides the user with a list of currently accepted as
valid names, as well as their higher classification. Unmatched taxon names are highlighted and the
user is prompted to thoroughly check the unmatched names.
Classification identifiers
Describes data: YES
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: YES
Freely distributable: NO
Open source: NO
Includes / applied to terrestrial species: NO
Includes / applied to marine species: YES
Includes / applied to fresh water species: NO
Provides Literature resources: NO
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: NO
Provides (bio-)Geographic area finder: NO
Provides Names finder: YES
Provides Authority search and match (name+year): YES
Provides Year match facility (with taxon requested): YES
Provides Extra searching facilities (row, column delimiter): YES
Provides Taxa range match facility (from to, or taxon x): YES
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: NO
Highlighting not matched names: YES
Taxonomic rank and nomenclature annotation:YES
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: YES
Output file as input file for other operations: YES
2. FishBase – Keys to fish classes (http://www.fishbase.org/identification/classlist.php).
Classification identifiers
Describes data: YES
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: NO
Freely distributable: NO
Open source: NO
Includes / applied to terrestrial species: NO
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: YES
Use of info and data from external resources (e.g. URL, other databases or file uploading): NO
Provides Glossary: YES
Provides (bio-)Geographic area finder: YES
Provides Names finder: NO
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: YES
Tool/service by geographic area: YES
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: YES
Taxon morphology info: YES
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: YES
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: NO
Output file as input file for other operations: NO
3. FishBase – FishBase-Keys of fish species identification
(http://www.fishbase.org/keys/allkeys.php): Keys to families and species identification by
geographic area.
Classification identifiers
Describes data: YES
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: NO
Freely distributable: NO
Open source: NO
Includes / applied to terrestrial species: NO
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: YES
Use of info and data from external resources (e.g. URL, other databases or file uploading): NO
Provides Glossary: YES
Provides (bio-)Geographic area finder: YES
Provides Names finder: NO
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: YES
Tool/service by geographic area: YES
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: YES
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: YES
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: NO
Output file as input file for other operations: NO
4. FishBase – Identification Using Morphometric Measurements
(http://www.fishbase.org/Identification/Morphometrics/centimeters/Index.php): It is an advanced
service of species identification by morphometrics which takes geographic, taxonomic and
morphometric information and retrieves possible matched species names along with their descriptions
and photos.
Classification identifiers
Describes data: YES
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: NO
Freely distributable: NO
Open source: NO
Includes / applied to terrestrial species: NO
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: YES
Use of info and data from external resources (e.g. URL, other databases or file uploading): NO
Provides Glossary: NO
Provides (bio-)Geographic area finder: YES
Provides Names finder: NO
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): YES
Provides Taxa range match facility (from to, or taxon x): YES
Interactive taxonomic key facility: YES
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: NO
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: YES
Taxon morphometrics: YES
Taxon photo match: YES
Taxon description: YES
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: NO
Output file as input file for other operations: NO.
5. FishBase – IncoFish (Shifting Baseline DatasetsSpecies)
(http://www.fishbase.org/Identification/Morphometrics/centimeters/Index.php): This is a
biogeographic service which takes information on specific datasets and on areas defined as Large
Marine Ecosystems (LMEs) and produces species distribution record tables and maps.
Classification identifiers
Describes data: YES
Describes meta-data: YES
Dynamical linking out facility with with reference systems: NO
File Validating options: NO
Freely distributable: NO
Open source: NO
Includes / applied to terrestrial species: NO
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: YES
Use of info and data from external resources (e.g. URL, other databases or file uploading): NO
Provides Glossary: NO
Provides (bio-)Geographic area finder: YES
Provides Names finder: YES
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): YES
Provides Extra searching facilities (row, column delimiter): YES
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: YES
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): YES
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: NO
Output file as input file for other operations: NO
6. FishBase – AquaMaps
(http://www.fishbase.org/Identification/Morphometrics/centimeters/Index.php): A service with
multiple tools aiming at the large-scale predictions, under certain scenarios, through model-based
approach of the currently known species distributions of marine species. Physico-chemical and
biological processes, such as temperature, salinity and primary productivity, are taken into account by
these models in order to produce the prediction maps.
Classification identifiers
Describes data: YES
Describes meta-data: YES
Dynamical linking out facility with with reference systems: NO
File Validating options: NO
Freely distributable: NO
Open source: NO
Includes / applied to terrestrial species: NO
Includes / applied to marine species: YES
Includes / applied to fresh water species: NO
Provides Literature resources: NO
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: NO
Provides (bio-)Geographic area finder: YES
Provides Names finder: YES
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): YES
Provides Extra searching facilities (row, column delimiter): YES
Provides Taxa range match facility (from to, or taxon x): YES
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: YES
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): YES
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): YES
Ecological quality indexing facility: NO
Output file options facility: YES
Output file as input file for other operations: YES
7. GBIF – Darwin Core Archive Assistant (Global Biodiversity Information Facility)
(http://tools.gbif.org/dwca-assistant/): DCAA is a web application that provides a simple interface
for describing the data elements a data provider serves to the GBIF network as basic text
files. It composes the appropriate XML descriptor file as defined in the Darwin Core Text
Guidelines to accompany the respective data.
Classification identifiers
Describes data: YES
Describes meta-data: YES
Dynamical linking out facility with with reference systems: NO
File Validating options: YES
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: YES
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: YES
Provides (bio-)Geographic area finder: NO
Provides Names finder: NO
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: YES
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: YES
Taxon morphometrics: YES
Taxon photo match: YES
Taxon description: YES
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: YES
Output file as input file for other operations: YES
8. GBIF - TaxonTagger (http://tools.gbif.org/taxontagger/): Web application that identifies,
highlights, and extracts scientific names from web pages and PDF documents. It uses the GBIF name
finder web services as it's name-finding engine and highlights names in a document and provides a
limited capacity to annotate the service output such as highlighting missed names, extending a find,
etc. The extracted list of species names can be subsequently exported as a simple DarwinCore list or
can be cross-referenced and mapped to the Catalogue of Life or other GBIF-indexed species lists to
output a complete classification of the taxa retrieved.
Classification identifiers
Describes data: NO
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: YES
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: YES
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: YES
Provides (bio-)Geographic area finder: NO
Provides Names finder: YES
Provides Authority search and match (name+year): YES
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): YES
Provides Taxa range match facility (from to, or taxon x): YES
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: NO
Highlighting not matched names: YES
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: YES
Output file as input file for other operations: YES
9. GBIF – ECAT Name Finder (http://tools.gbif.org/namefinder/): An html client to the name finding
web services hosted at GBIF. This service locates and extracts scientific names in a text document. It
is functionally linked to the global name architecture (GNA).
Classification identifiers
Describes data: NO
Describes meta-data: NO
Dynamical linking out facility with with reference systems: YES
File Validating options: NO
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: NO
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: NO
Provides (bio-)Geographic area finder: NO
Provides Names finder: YES
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: NO
Highlighting not matched names: YES
Taxonomic rank and nomenclature annotation: YES
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: NO
Output file as input file for other operations: NO
10. GBIF – GPAAMP (Global Protected Areas Assessment and Monitoring Pilot viewer)
(http://tools.gbif.org/gpaamp-demo/): This is a visualizing tool of information from disparate sources
delivered through standard-based web services.
Classification identifiers
Describes data: NO
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: NO
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: NO
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: NO
Provides (bio-)Geographic area finder: NO
Provides Names finder: NO
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): YES
Provides Extra searching facilities (row, column delimiter): YES
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: YES
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): YES
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): YES
Ecological quality indexing facility: NO
Output file options facility: YES
Output file as input file for other operations: YES
11. GBIF – BIDDSAT (Biodiversity Datasets Assessment Tool)
(http://www.gbif.org/orc/?doc_id=4696): Online tool where the user can analyze datasets published
and registered in the GBIF network. Selection options include metrics based on different variables
(e.g. taxonomy, type of record) and automatically produce maps and relevant diagrams.
Classification identifiers
Describes data: YES
Describes meta-data: YES
Dynamical linking out facility with with reference systems: NO
File Validating options: NO
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: NO
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: NO
Provides (bio-)Geographic area finder: NO
Provides Names finder: NO
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): YES
Provides Extra searching facilities (row, column delimiter): YES
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: NO
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): YES
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): YES
Ecological quality indexing facility: NO
Output file options facility: NO
Output file as input file for other operations: YES
12. uBIO – LinkIT (Universal Biological Indexer and Organizer)
(http://www.ubio.org/tools/linkit.php): This tool allows the user to develop automated dynamic link
outs from names in his/her own pages, databases, and texts to expert systems.
Classification identifiers
Describes data: YES
Describes meta-data: NO
Dynamical linking out facility with with reference systems: YES
File Validating options: YES
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: YES
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: NO
Provides (bio-)Geographic area finder: NO
Provides Names finder: YES
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: NO
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: YES
Output file as input file for other operations: YES
13. uBIO - FindIT (http://www.ubio.org/tools/recognize.php): Scientific name identification in text.
Classification identifiers
Describes data: YES
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: YES
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: NO
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: NO
Provides (bio-)Geographic area finder: NO
Provides Names finder: YES
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): YES
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: NO
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: YES
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: NO
Output file as input file for other operations: NO
14. uBIO – Author Abbreviation Resolver (http://www.ubio.org/apps/authors/index.php): Web
service and database of variations throughout the recording of author and taxonomic names in the
literature.
Classification identifiers
Describes data: NO
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: NO
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: NO
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: NO
Provides (bio-)Geographic area finder: NO
Provides Names finder: NO
Provides Authority search and match (name+year): YES
Provides Year match facility (with taxon requested): YES
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: NO
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: NO
Output file as input file for other operations: NO
15. uBIO – TNS Name Mapper (http://www.ubio.org/services/mapper/index2.php): This web tool
superimposes lists of names against multiple checklists and classifications.
Classification identifiers
Describes data: NO
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: NO
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: NO
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: NO
Provides (bio-)Geographic area finder: NO
Provides Names finder: YES
Provides Authority search and match (name+year): YES
Provides Year match facility (with taxon requested): YES
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: NO
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: YES
Output file as input file for other operations: YES
16. uBIO – ParseIT (http://www.ubio.org/tools/explode.php): It receives complex scientific names and
breaks them down to its component parts. Useful for the name variants.
Classification identifiers
Describes data: NO
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: NO
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: NO
Use of info and data from external resources (e.g. URL, other databases or file uploading): NO
Provides Glossary: NO
Provides (bio-)Geographic area finder: NO
Provides Names finder: YES
Provides Authority search and match (name+year): YES
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: NO
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: YES
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: NO
Output file as input file for other operations: NO
17. uBIO – CanonizeIT (http://www.ubio.org/tools/canonize.php): The tool receives any scientific
name and author combination and provides the canonical form of the name, that is the primary
nomenclatural components of a scietific name combination that can be used for comparing lexical
equivalence among name strings.
Classification identifiers
Describes data: NO
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: NO
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: NO
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: NO
Provides (bio-)Geographic area finder: NO
Provides Names finder: YES
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: NO
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: NO
Output file as input file for other operations: NO
18. uBIO – x:ID (http://www.ubio.org/index.php?pagename=XID/key): This tool provides the
opportunity to the users to build their own web-based diagnostic or identification keys and run them
over locally or on the internet.
Classification identifiers
Describes data: YES
Describes meta-data: YES
Dynamical linking out facility with with reference systems: NO
File Validating options: YES
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: YES
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: NO
Provides (bio-)Geographic area finder: NO
Provides Names finder: NO
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: YES
Dichotomous/pictorial key facility: YES
Tool/service by geographic area: NO
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: YES
Taxon morphometrics: YES
Taxon photo match: YES
Taxon description: YES
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: NO
Output file as input file for other operations: NO
19. ALA - Spatial Portal (Atlas of Living Australia) (http://spatial.ala.org.au/): Allows the user to
create various maps on-the-fly, according to specified criteria or uploaded species lists.
Classification identifiers
Describes data: YES
Describes meta-data: YES
Dynamical linking out facility with with reference systems: NO
File Validating options: NO
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: NO
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: NO
Provides (bio-)Geographic area finder: YES
Provides Names finder: YES
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): YES
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: YES
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): YES
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: YES
Output file as input file for other operations: YES
20. OBIS - mapping tool (Ocean Biogeographi Information System) (http://iobis.org/mapper/):
Allows the user to query the database and create various distribution maps on-the-fly (species
distribution datasets).
Classification identifiers
Describes data: YES
Describes meta-data: YES
Dynamical linking out facility with with reference systems: NO
File Validating options: NO
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: NO
Includes / applied to marine species: YES
Includes / applied to fresh water species: NO
Provides Literature resources: NO
Use of info and data from external resources (e.g. URL, other databases or file uploading): NO
Provides Glossary: YES
Provides (bio-)Geographic area finder: YES
Provides Names finder: YES
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): YES
Provides Extra searching facilities (row, column delimiter): YES
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: YES
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): YES
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: NO
Output file options facility: YES
Output file as input file for other operations: YES
21. IBEM-ecological quality index (indice de biodiversité des étangs et mares)
(http://campus.hesge.ch/ibem/welcome.asp): Calculates certain indices on-the-fly according to
parameters chosen by the user, focus on lakes.
Classification identifiers
Describes data: NO
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: YES
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: NO
Includes / applied to marine species: NO
Includes / applied to fresh water species: YES
Provides Literature resources: NO
Use of info and data from external resources (e.g. URL, other databases or file uploading): YES
Provides Glossary: NO
Provides (bio-)Geographic area finder: NO
Provides Names finder: NO
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: NO
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): NO
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): NO
Ecological quality indexing facility: YES
Output file options facility: NO
Output file as input file for other operations: NO
22. mMWeb – MAMS (multi-models web - Marble Algorithm Modeling System)
(http://mmweb.animal.net.cn/; http://mmweb.animal.net.cn/alglist.jsp): This service provides an
integrated spatial analysis algorithm for predicting distributions of a given organism. MAMS extracts
and analyzes data from the occurrence localities of a given species and is a web-based application.
Classification identifiers
Describes data: NO
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: YES
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: YES
Use of info and data from external resources (e.g. URL, other databases or file uploading): NO
Provides Glossary: NO
Provides (bio-)Geographic area finder: YES
Provides Names finder: NO
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: YES
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): YES
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): YES
Ecological quality indexing facility: NO
Output file options facility: YES
Output file as input file for other operations: YES
23. mMWeb – CSM (multi-models web – Climate Space Model)
(http://mmweb.animal.net.cn/index.jsp): This service is a principle components based algorithm.
The component selection processed in this algorithm implementation is based on the Broken-Stick
cutoff where any component with an eigenvalue less than (n stddevs above a randomised sample) is
discarded.
Classification identifiers
Describes data: NO
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: YES
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: YES
Use of info and data from external resources (e.g. URL, other databases or file uploading): NO
Provides Glossary: NO
Provides (bio-)Geographic area finder: YES
Provides Names finder: NO
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: YES
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): YES
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): YES
Ecological quality indexing facility: NO
Output file options facility: YES
Output file as input file for other operations: YES
24. mMWeb – ENFA (multi-models web – Ecological Niche Factor Analysis)
(http://mmweb.animal.net.cn/index.jsp): This service uses a modified principal components
analysis to develop a model based on presence only data. The observed environment is compared to
the background data of the study area. The analysis produces factors similar to a PCA.
Classification identifiers
Describes data: NO
Describes meta-data: NO
Dynamical linking out facility with with reference systems: NO
File Validating options: YES
Freely distributable: YES
Open source: YES
Includes / applied to terrestrial species: YES
Includes / applied to marine species: YES
Includes / applied to fresh water species: YES
Provides Literature resources: YES
Use of info and data from external resources (e.g. URL, other databases or file uploading): NO
Provides Glossary: NO
Provides (bio-)Geographic area finder: YES
Provides Names finder: NO
Provides Authority search and match (name+year): NO
Provides Year match facility (with taxon requested): NO
Provides Extra searching facilities (row, column delimiter): NO
Provides Taxa range match facility (from to, or taxon x): NO
Interactive taxonomic key facility: NO
Dichotomous/pictorial key facility: NO
Tool/service by geographic area: YES
Highlighting not matched names: NO
Taxonomic rank and nomenclature annotation: NO
Taxon morphology info: NO
Taxon morphometrics: NO
Taxon photo match: NO
Taxon description: NO
Mapping tools (lat-long, FAO, biodiversity, etc): YES
Modeling facility on mapping (climate change, invasive species, ecological niche, etc): YES
Ecological quality indexing facility: NO
Output file options facility: YES
Output file as input file for other operations: YES
Multivariate analysis of the coded data
The ultimate purpose of the coding of these services and tools available is to explore any
commonalities and/or complementary aspects in their operational features and functionality. For this
reason, a features-by-service(/tool) matrix was constructed, based on the coded data presented
above. Subsequently, the Jaccard similarity coefficient was applied in order to construct the triangular
similarity matrix which describes similarities between all possible pairs of the web services and tools
taken into account in the context of this report. The standard hierarchical cluster analysis and the nonmetric mutli-dimensional scaling (nMDS) algorithms were applied to this matrix in order to visualize
their relationships as similarity dendrogram and MDS plot.
The assumed hypothesis is that there must be two factors that can affect the relationships
between the studied web sites and tools: (a) the web site development, that is the services and tools
developed under the same site, hence framework, are supposed to appear more similar to each other
than to those from the remainder web sites; (b) the processing and analytical function they carry out,
which means that services and tools developed to carry out similar functions or client needs must be
similar to each other. In order to statistically test the above two assumptions the permutational
mutlivariate analysis of variance (PERMANOVA) was performed to the same similarity matrix.
No clear separation of the services and tools can be seen in the following MDS plot.
However, the cluster analysis dendrogram is showing a much more clear picture of the
interrelations of the various services and tools.
Here one can identify clusters of similar services, such as those included in the mMWeb site or
the ones that offer mapping options (FishBase, OBIS, and ALA). However, the testing of the above
assumptions is only carried out through the application of the PERMANOVA .
Source
df
SS
MS
Website
Function
Website x Function
6
4
11980
9960.4
1996.7
2490.1
2.4312
3.032
0.004
0.004
996
998
1
11
23
3277.5
9034.2
51033
3277.5
821.29
3.9907
0.003
999
Res
Total
Pseudo-F p-Value
Permutation No
In the above table with the results of the PERMANOVA it is clearly shown that both factors, as
well as their combination, seem to have a significant effect on the relationships of the analyzed web
services and tools.
Conclusions
The analysis of this report shows that the existing tools and services in the web sites of the
major projects, initiatives, fora and organizations show many similarities in their features which
describe their operation and their input and output functions.
Both the web site and the function of the services and tools seem to affect their interrelations.
This simply means that there occur many commonalities in their functions which are derived by the
fact that they have been built under the same framework (web site) or to address similar needs of their
clients.
These results should be taken into account in the development of ViBRANT's services and tools
and some elements in their performance, such as standard protocols and speed, should perhaps take a
priority.