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date	2009.11.06.20.03.00;	author CynthiaParr;	state Exp;
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---+ Background Material for SPM working session

---++ Possible changes to existing terms and definitions of Info Items

See OpenIssues and also feel free to add your comments and information here.

 See also [[PlaziFinalReport]] for issues identified by the [[PlaziEOLProject]]

See also [[%ATTACHURL%/SPM_and_the_SPRAT_structure.docx][SPM_and_the_SPRAT_structure.docx]],  [[%ATTACHURL%/Attachment_A_SPMvsSPRAT.xlsx][Attachment_A_SPMvsSPRAT.xlsx]], and  [[%ATTACHURL%/Attach_B_spm_vs_sprat.docx][Attach_B_spm_vs_sprat.docx]]:
: Analysis by Nicole Coomb on SPM and SPRAT

For a history of how certain terms got to be part of the working version of Species Profile Model, see [[http://wiki.tdwg.org/twiki/bin/view/SPM/SpeciesProfileModel]]

There are some definitions of proposed InfoItems here: http://wiki.gbif.org/dadiwiki/images/speciesmodel/speciesModelElements.xls
but none of the InfoItems appear to have comments (definitions) in the actual RDF representation. Encyclopedia of Life has developed definitions in order to guide the usage of the vocabulary for its use, as seen in EOL's schema glossary on page  http://eol.org/files/pdfs/docs/EOL_Transfer_Schema_Glossary.pdf  . However, some of these terms and definitions have proven difficult to apply. Below is a list of InfoItems (subject categories, in EOL's parlance) and the changes and/or definitions that Cyndy Parr would like to propose.

 *Associations*: Predator‐prey; host‐parasite, pollinators, symbiosis, mutualism, commensalism; hybridisation, ...

   * Change: Emphasize narratives, not list. To be effective, perhaps associatedTaxa should be expanded to specify nature of association, e.g. parasiteOf, hostOf, preyOf, predatorOf, causesDiseaseOf etc. 
   * Proposed new definition: Descriptions (in narrative form) of taxa that interact with the subject taxon. Includes explicit reference to the kind of ecological interaction: Predator/prey; host/parasite, pollinators, symbiosis, mutualism, commensalism; hybridisation. List taxa using the associatedTaxa property. 

*Behaviour*: Covers actions and reactions of organism in relation to its biotic and abiotic environment.

   * Proposed new definition: Description of behaviour and behaviour patterns of an organism, including actions and reactions of organism in relation to its biotic and abiotic environment. Includes communication, perception, modes and mechanisms of locomotion, as well as long term strategies (except mating and reproductive strategies, covered under reproduction).

*Conservation Status*: A description of the likelihood of the species becoming extinct in the present day or in the near future.

   * Proposed new definition: A description of the likelihood of the species becoming extinct in the present day or in the near future. Population size is treated under Population Biology, and trends in population sizes are treated under Trends. However, this is the preferred element if an object includes all of these things and details about conservation listings.

*Cyclicity*: A state or condition characterised by regular repetition in time.

   * Proposed new definition: Description of biorhythms, whether on the scale of seconds, hours, days, or seasons. Those states or conditions characterised by regular repetition in time. Could also cover phenomena such as chewing rates. Life cycles are treated in the Life Cycle term. Seasonal migration and reproduction are usually treated separately.

*Cytology*: Cell biology: formation, structure and function of cells.

*Diagnostic Description*: Distinguishing feature of this taxon from its closest relatives.

   * Proposed new definition: Lists the features that distinguish this taxon from its closest relatives. May include but is not restricted to synapomorphies.

*Diseases*: Diseases of organisms.

   * Proposed new definition: Description of diseases that the organism is subject to. Disease-causing organisms can also be listed under associations.

*Dispersal*: Dispersal strategies and mechanisms.

   * Proposed new definition: Description of the methods, circumstances, and timing of dispersal (includes both natal dispersal and interbreeding dispersal?)

*Distribution*: Covers ranges, e.g., a global range, or a narrower one; may be biogeographical, political or other (e.g., managed areas like conservencies); endemism; native or exotic; ref : Darwin Core Geospatial extension

   * Proposed new definition: Covers ranges, e.g., a global range, or a narrower one; may be biogeographical, political or other (e.g., managed areas like conservencies); endemism; native or exotic; ref  Darwin Core Geospatial extension. Does not include altitudinal distribution, which is covered under Habitat.

*Ecology*: 

   * Can't find a good definition right now!

*Evolution*: Phylogenetic information relating to the taxon

   * Change: consider separating taxonomy from evolution and including a new term, Taxonomy (or Systematics); otherwise
   * Proposed new definition: Description of phylogenetic and systematic treatments of the taxon.

*General Description*: A comprehensive description of the characteristics of the taxon.

   * Change: the intent of this InfoItem was never very clear. It may be that a better label is needed such as "Comprehensive definition"
   * Proposed new definition: A comprehensive description of the characteristics of the taxon. To be used primarily when many of the subject categories are treated together in one object, but at length. Taxon biology (see below) is to be used if a brief summary.

*Genetics*: Including karyotypes.

   * Proposed new definition: Information on the genetics of the taxon, including karyotypes, barcoding status, whole genome sequencing status, ploidy.

*Growth*: Rate; parameters; allometries.

   * Proposed new definition: Description of growth rates, allometries, parameters known to be predictive, morphometrics. Can also include hypotheses of paedomorphy or neoteny, etc.

*Habitat*: Includes realm (e.g. Terrestrial etc) and climatic information (e.g. Boreal); also includes requirements and tolerances; horizontal and vertical distribution.

   * Proposed new definition: Includes realm (e.g Terrestrial etc) and climatic information (e.g Boreal); also includes requirements and tolerances; horizontal and vertical (altitudinal) distribution.

*Legislation*: Legal regulations or statutes relating to the taxon.

*Life Cycle*: Obligatory developmental transformations.

   * Proposed new definition: Defines and describes obligatory developmental transformations. Includes metamorphosis, instars, gametophyte/embryophytes, transitions from sessile to mobile forms. Discusses timing. Morphology of each form is usually described in morphological descriptions.

*Life Expectancy*: The average period an organism can be expected to survive.

   * Proposed new definition: Any information on longevity, including the average period an organism can be expected to survive.

*Look Alikes*: Other taxa that this taxon may be confused with. Common in invasive species communities.

   * Change: Consider changing the label of this InfoItem. Or if this is to be a list, then perhaps it should take the associatedTaxon property.
   * Proposed new definition: Other taxa that this taxon may be confused with, and characters useful for their differentiation. Useful for identification and comparison. Common in invasive species communities. List taxa using associatedTaxon property.

*Management*: A statement about the level of need to manage a taxon which can be related to a piece of legislation, e.g., a CITES list.

   * Change: In practice this is not well differentiated from Procedures. Proposed they be combined into "Management procedures."
   * Proposed new definition: Describes techniques and goals used in management of species. May include management relative to a piece of legislation, e.g., a CITES list. 

*Migration*: Periodic movement of organisms from one locality to another (e.g., for breeding).

   * Proposed new definition: Description of the periodic movement of organisms from one locality to another (e.g., for breeding). Usually includes locality, timing, and hypothesized purpose.

*Molecular Biology*: Includes genomic, proteomic and biochemistry (e.g. Toxicity).

   * Proposed new definition: Includes proteomic and biochemistry (e.g Toxicity). Genomic information is usually treated under Genetics.

*Morphology*: The appearance of the taxon; e.g. Habit; anatomy (the branch of morphology that deals with structure of animals).

   * Proposed new definition: Description of the appearance of the taxon; e.g body plan, shape and color of external features, typical postures. May be referred to as or include habit, or anatomy.

*Physiology*: An account of the physiological processes.

   * Proposed new definition: Description of physiological processes. Includes metabolic rates, and systems such as circulation, respiration, excretion, immunity, neurophysiology.

*Population Biology*: Includes abundance information.

   * Proposed new definition: Includes abundance information (population size, density) and demographics (e.g. age stratification).

*Procedures*: Deals with how you go about managing this taxon; what are the known threats to this taxon?

   * Change: In practice this is not well differentiated from Procedures, and threats are treated below. Proposed they be combined into "Management procedures."

*Reproduction*: Reproduction cues, strategies, restraints.

   * Proposed new definition: Description of reproductive physiology and behavior, including mating and life history variables. Includes cues, strategies, restraints, rates.

*Risk Statement*: Includes invasiveness, impacts.

   * Change: This has been ambiguous -- is it only a risk to other species if it is present, or also the risk to other species if it is not present. May need to consider adding a term to separate.
    * Proposed new definition: Negative impacts on humans, communities. [This may also include impacts on ecosystems should the organism decline or be extirpated]

*Size*: Average size, max, range; type of size (perimeter, length, volume, weight ...)

   * Proposed new definition: Narrative description of average size, max, range; type of size (perimeter, length, volume, weight ...). 

*Taxon Biology*: An account of the biology of the taxon.

   * Change: The intent of this element has been unclear. Biology is very broad; a comprehensive description already can fit under "General Description." We propose changing this to a "Brief description" or "Overview."
   * Proposed new definition: Summary or overview of all aspects of an organism's biology. 

*Threats*: The threats to which this taxon is subject.

*Trends*: An indication of whether a population is stable, or increasing or decreasing.

*Trophic Strategy*: Include nutritional aspects, diet, position in food network.

   * Proposed new definition: Summaries general nature of feeding interactions. For example, basic mode of nutrient uptake (autotrophy, heterotrophy, coprophagy, saprophagy), position in food network (top predator, primary producer, consumer), diet categorization (detritovore, omnivore, carnivore, herbivore). Specific taxa are treated under Associations (specifying predators or prey) and associatiedTaxa.

*Uses*: Relationships to humans; ref: Cook “Economic Botany”

   * Proposed new definition: Benefits for humans. ref Cook "Economic Botany" Can include ecosystem services. However, benefits to ecosystems not specific to humans are best treated under Risk statement (what happens when the organism is removed)



-- Main.CynthiaParr - 04 Nov 2009

---++ Mechanisms for adding new terms to SPM

We should not be aiming to make SPM unwieldy and large, but there may be cases where a term is not covered well by the others and will be widely useful. We need a mechanism for proposing and debating and deciding on which terms are added to the SPM core. In some ways this depends on the way we intend to maintain SPM. 

There is a version of SPM set up on the TDWG ontology server: http://rs.tdwg.org/ontology/voc/SpeciesProfileModel.rdf and it appears that this has some discussion capability. Has anybody used this for SPM or any other standard?

Roger Hyam wrote early this summer:

On Wed, Jun 10, 2009 at 10:33 AM, Roger Hyam <rogerhyam@@mac.com> wrote:
> Hi Cyndy,  I am taking on myself to have a go at clearing up the http://rs.tdwg.org/ontology space. We have some classes in here that talk about the species profile model.  I was wondering which of these are actually in use and which I can change.  http://rs.tdwg.org/ontology/voc/SpeciesProfileModel . Can you summarize where SPM is in terms of term definition?
Is anyone ever going to do inference over this stuff or would it be better to run a SKOS vocabulary of terms to tag species accounts with? What do you think? Who should I talk to about this? 

-- Main.CynthiaParr - 04 Nov 2009

---++ GBIF vocabulary server

GBIF is developing this and it may be useful for SPM or SPM users.

---++ Use of Thomson Reuters subject thesaurus (term vocabularies)

Donald Hobern (Atlas of Living Australia) called a few of us together at the e-Biosphere '09 London meeting to briefly discuss the possibility of TDWG using the subject thesaurus developed by Thomson Reuters as a means of providing a more detailed vocabulary for marking up or tagging documents that are currently only served by the relatively few, high-level SPM subject terms, and to provide a basis for text mining. The following correspondence are excerpts from follow up .

-- Main.CynthiaParr - 04 Nov 2009

Donald Hobern (Atlas of Living Australia, August 12)

TDWG has for some time been interested in the development of standards to assist biodiversity-related projects in making all their information resources more accessible for reuse in new contexts.  One part of this has been the work on the "Species Profile Model".  The idea here is to make it possible for any web database or set of web pages to tag their fields with terms which identify the topics they address.  At its crudest this could in theory just be a set of well-defined, non-overlapping major subject areas (distribution, identification, morphology, etc.) although it seems unlikely that any such single-level categorisation will be flexible enough to meet the requirements.  A rich hierarchical thesaurus would be much more appropriate.  Assigning URIs to every term in such a thesaurus would then allow us to tag blocks of text or structured data with pointers to the term or terms which best express their content.  Such an approach could be embedded in HTML templates to allow crawlers to understand more of the semantic composition of a page.  The same terms could be used as labels for database fields, allowing us to use the same kind of models that we have used with DiGIR and TAPIR and specimen data to allow a user e.g. to send FishBase a request for all information on distribution for any species in the genus Gadus.  Consuming applications could decide whether or not to include data tagged to a low-level hierarchy term in addressing a request for a more general term, or indeed whether to direct users to data tagged with a higher-level term in the hope that it may still contain something relevant.  This should be a useful tool for ALA, EOL, FishBase, etc. to share and reuse all their content with as much precision as possible.

<EFBFBD>amonn <20> Tuama (GBIF) Aug 14

GBIF is interested in supporting this endeavour. Having a well defined, web-accessible subject thesaurus for biodiversity resources would be a great asset, and as Donald mentions below, it would be good if it could be extended through shared community involvement. One immediate use in the GBIF data portal would be for the tagging of metadata documents.

Nigel Robinson (Thomson Reuters) October 22

In principle we have no issues with licensing the thesaurus (at little/no cost) in exchange for collaboration, credit, provided there is some demonstrable benefit I can show up the line here. We would issue a license to govern the relationship and provide protection to both parties &#8211; as we did with GBIF.

---++ Ratification process


---++ Relationship to TDWG ontology and eBiosphere roadmap


  

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*Risk Statement: Includes invasiveness, impacts.
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   * Associations: Predator&#8208;prey; host&#8208;parasite, pollinators, symbiosis, mutualism, commensalism; hybridisation, ...
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     Change: Emphasize narratives, not list.
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     Proposed new definition: Descriptions (in narrative form) of taxa that interact with the subject taxon. Includes explicit reference to the kind of ecological interaction: Predator/prey; host/parasite, pollinators, symbiosis, mutualism, commensalism; hybridisation. Lists can be handled using the associatedTaxa property. (need help with this) 
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   * Behaviour: Covers actions and reactions of organism in relation to its biotic and abiotic environment.
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Proposed new definition: Description of behaviour and behaviour patterns of an organism, including actions and reactions of organism in relation to its biotic and abiotic environment. Includes communication, perception, modes and mechanisms of locomotion, as well as long term strategies (except mating and reproductive strategies, covered under reproduction).
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   * Conservation Status: A description of the likelihood of the species becoming extinct in the present day or in the near future.
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Proposed new definition: A description of the likelihood of the species becoming extinct in the present day or in the near future. Population size is treated under Population Biology, and trends in population sizes are treated under Trends. However, this is the preferred element if an object includes all of these things and details about conservation listings.
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   * Cyclicity: A state or condition characterised by regular repetition in time.
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Proposed new definition: Description of biorhythms, whether on the scale of seconds, hours, days, or seasons. Those states or conditions characterised by regular repetition in time. Could also cover phenomena such as chewing rates. Life cycles are treated in the Life Cycle term. Seasonal migration and reproduction are usually treated separately.
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   * Cytology: Cell biology: formation, structure and function of cells.
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   * Diagnostic Description: Distinguishing feature of this taxon from its closest relatives.
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Proposed new definition: Lists the features that distinguish this taxon from its closest relatives. May include but is not restricted to synapomorphies.
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   * Diseases: Diseases of organisms.
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Proposed new definition: Description of diseases that the organism is subject to. Disease-causing organisms can also be listed under associations.
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   * Dispersal: Dispersal strategies and mechanisms.
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Proposed new definition: Description of the methods, circumstances, and timing of dispersal (includes both natal dispersal and interbreeding dispersal?)
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   * Distribution: Covers ranges, e.g., a global range, or a narrower one; may be biogeographical, political or other (e.g., managed areas like conservencies); endemism; native or exotic; ref : Darwin Core Geospatial extension
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Proposed new definition: Covers ranges, e.g., a global range, or a narrower one; may be biogeographical, political or other (e.g., managed areas like conservencies); endemism; native or exotic; ref  Darwin Core Geospatial extension. Does not include altitudinal distribution, which is covered under Habitat.
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   * Evolution: Phylogenetic information relating to the taxon
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Change: consider separating taxonomy from evolution and including a new term, Taxonomy (or Systematics); otherwise
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Proposed new definition: Description of phylogenetic and systematic treatments of the taxon.
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   * General Description: A comprehensive description of the characteristics of the taxon.
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Change: the intent of this InfoItem was never very clear. It may be that a better label is needed.
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Proposed new definition: A comprehensive description of the characteristics of the taxon. To be used primarily when many of the subject categories are treated together in one object, but at length. Taxon biology (see below) is to be used if a brief summary.
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   * Genetics: Including karyotypes.
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Proposed new definition: Information on the genetics of the taxon, including karyotypes, barcoding status, whole genome sequencing status, ploidy.
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   * Growth: Rate; parameters; allometries.
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Proposed new definition: Description of growth rates, allometries, parameters known to be predictive, morphometrics. Can also include hypotheses of paedomorphy or neoteny, etc.
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   * Habitat: Includes realm (e.g. Terrestrial etc) and climatic information (e.g. Boreal); also includes requirements and tolerances; horizontal and vertical distribution.
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Proposed new definition: Includes realm (e.g Terrestrial etc) and climatic information (e.g Boreal); also includes requirements and tolerances; horizontal and vertical (altitudinal) distribution.
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   * Legislation: Legal regulations or statutes relating to the taxon.
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   * Life Cycle: Obligatory developmental transformations.
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Proposed new definition: Defines and describes obligatory developmental transformations. Includes metamorphosis, instars, gametophyte/embryophytes, transitions from sessile to mobile forms. Discusses timing. Morphology usually described in morphological descriptions.
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   * Life Expectancy: The average period an organism can be expected to survive.
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Proposed new definition: Any information on longevity, including the average period an organism can be expected to survive.
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   * Look Alikes: Other taxa that this taxon may be confused with. Common in invasive species communities.
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Change: Consider changing the label of this InfoItem.
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   * Management: A statement about the level of need to manage a taxon which can be related to a piece of legislation, e.g., a CITES list.
   * Migration: Periodic movement of organisms from one locality to another (e.g., for breeding).
   * Molecular Biology: Includes genomic, proteomic and biochemistry (e.g. Toxicity).
   * Morphology: The appearance of the taxon; e.g. Habit; anatomy (the branch of morphology that deals with structure of animals).
   * Physiology: An account of the physiological processes.
   * Population Biology: Includes abundance information.
   * Procedures: Deals with how you go about managing this taxon; what are the known threats to this taxon?
   * Reproduction: Reproduction cues, strategies, restraints.
   * Risk Statement: Includes invasiveness, impacts.
   * Size: Average size, max, range; type of size (perimeter, length, volume, weight ...)
   * Taxon Biology: An account of the biology of the taxon.
   * Threats: The threats to which this taxon is subject.
   * Trends: An indication of whether a population is stable, or increasing or decreasing.
   * Trophic Strategy: Include nutritional aspects, diet, position in food network.
   * Uses: Relationships to humans; ref: Cook &#8220;Economic Botany&#8221;
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-- Main.CynthiaParr - 03 Nov 2009
@