1. Do we specify taxonomic hierarchy or just kingdom/scientific name
- Just kingdom/scientific name for now
2.Can ask service: do you supported hierarchical taxon queries?
- Later addition
3. Need a method to determine if a record is from its original data set or is a duplicate
4. Need a method to determine the original source of a duplicated record
5. Need to include LSIDs for each record. Will LSIDs address issues 3 and 4?
6. The Metadata in TAPIR uses' 2 letter language codes. Should we do the same?
7. Should we add "Debugging" as a format parameter?
1. PROPOSAL: Add a new data model for EnvironmentalInfo?
Status: Proposed
This datamodel will help distinguish between species that occur in natural or human modified environments, and/or in freshwater, brackish, marine and terrestrial habitats. Multiple values are possible. These concepts are different from EcosystemImpacted? and HabitatImpacted? (a terrestrial species can impact aquatic environments). At the GISIN portal someone could filter by ‘terrestrial‘ to get all terrestrial species – whether or not the habitat impacted might be both terrestrial and aquatic.
EnvironmentalInfo supports the following additional Concepts: Possible values for the additional Concepts are listed in the table.
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| SpeciesEnvironment | No | String | Natural, HumanModified? | The environment in which the species occurs |
| SpeciesBiome | No | String | Freshwater, Brackish, Marine, Terrestrial | The biome in which the species occurs |
2. PROPOSAL: Change Harmful back to Invasive in BioStatus?
Status: Proposed
Discussion: Many believe that ‘Harm’ is subjective and that it is the culmination of the invasion process, which begins with establishment, then persistence and spread. If we provided the word ‘Invasive’ instead of ‘Harmful’ in the BioStatus? concept, most providers would be able to map to its possible values, but each provider might mean something different. The key differences are between;
ONE: Scientific uses of the word ‘Invasive’ meaning ability to spread (i.e. Distribution = Widespread or Moderate, and/or Abundance= Dominant or Common) and
TWO: Policy uses of the word ‘Invasive’ meaning ability to cause harm.
Different meanings or usages can be deduced from the additional concepts for which data is provided. Currently, the first group can select ‘Invasive’ then map their data to Distribution = (Widespread or Moderate), and/or Abundance= (Dominant or Common) and/or Harmful= (Yes or Potentially).
The second group can select ‘Invasive’ then map their data to ImpactStatus? concepts as well as those of group 1.
More Discussion: Folks had major issues with the term “Invasive”. We decided to use “Harmful=Yes”. However, invasiveness data would not be mapped to the ‘Harmful’ concept if there is only evidence of establishment, persistence and spread (e.g. when harm has not been confirmed). A search at the GISIN portal on Harmful = yes would miss this invasiveness data.
BioStatuses support the following additional Concepts. Possible values for the Concepts are listed below this table.
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| Source | No | String | Citation for the source of the data | |
| Origin | Yes | String | Indigenous, Nonindigenous, Unknown | Whether the species is considered to be native to a particular location or not. |
| Presence | Yes | String | Absent, Sometimes, Present, Unknown | There is supporting evidence to show the species is present within the valid date |
| Persistence | No | String | Persistent, Temporary [let's delete this value. MB], Transient, DiedOut?, Unknown | How successful the organism is at surviving and reproducing |
| Distribution | No | String | Widespread, Moderate, Localized, Unknown | Whether the species is limited to a local area or covers vast tracks of land or water |
| Abundance | No | String | Dominant, Common, Rare, Zero, Unknown | How abundant the organism is |
| Trend | No | String | Expanding, Stable, Declining, Unknown | Whether the range of the organism is increasing or decreasing |
| RateOfSpread | No | String | Rapid, Moderate, Slow, Unknown | How quickly the range of the organism is expanding |
| Invasive | Yes | String | Yes, No, Potentially, Unknown | Whether the organism causes concern. 'Spread' information is dealt with in BioStatus. 'Harm' information is dealt with in the ImpactStatus? Element as are Environmental versus Livelihood and HumanHealth impacts.>? element |
| RegulartoryListing | No | String | Prohibited, Restricted, NotConsidered, Unknown | The legal regulatory status of the organism |
3. ImpactStatus?
3.1 PROPOSAL: Introduce an ImpactMechanism? concept
Status: Proposed
Introduce an ImpactMechanism? concept to handle information about competition, predation, etc. i.e. how IAS damage species habitats and ecosystems. This kind of information is widely available and ImpactMechanism? allows us to make assumptions about which kinds of native species may be threatened.
3.2 PROPOSAL: Change HarmType? values from HarmfulToEconomy? to HarmfulToLivelihoods?.
Status: Proposed
3.3 PROPOSAL: Make HabitatImpacted? non-mandatory
Status: Proposed
ImpactStatuses support the following additional Concepts:
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| BiomeImpacted | No | String | Freshwater, Brackish, Marine, Terrestrial | The ecosystem type being impacted (can be more than one). |
| EnvironmentImpacted | No | String | Natural, HumanModified? | Type of environment being impacted |
| HarmType | No | String | HarmfulToEnvironment, HarmfulToLivelihoods?HarmfulToHumanHealth? | What values the species is impacting (can be more than one) |
| ImpactLevel | No | String | Habitat, Ecosystem | Level at which impact is occuring (can be more than one) |
| SpeciesImpacted | No | String | (undefined) | Use scientific name (can be more than one) |
| HabitatImpacted | No | String | (undefined) | Description of habitat impacted |
| EcosystemImpacted | No | String | (undefined) | Description of the ecosystem being impacted |
| *EcosystemServicesImpacted | No | String | Provisioning, Regulating, Cultural, Supporting | Ecosystem services are the benefits that people obtain from ecosystems (can be more than one). |
| LivelihoodValuesImpacted | No | String | (undefined) | Description of impacts on livelihoods. |
| HumanHealthValuesImpacted | No | String | (undefined) | Description of impacts on human health. |
| ImpactMechanism | No | String | Allergenic, Competition, DiseaseTransmission?, Herbivory, Hybridisation, InteractionWithOtherInvasiveSpecies?, Pathogenic/Parasite, PhysicalDisturbance?, Predation, SoilTransformation?, Transpiration, Other, Unknown | Mechanism by which negative impacts occur |
| *ImpactStrength | No | String | Massive, Strong, Moderate, Weak, None, Unknown | How strong the impact is |
| ImpactCost | No | String | (undefined) | Description of cost and either estimated or actual monetary value. |
| ImpactBenefit | No | String | (undefined) | Description of benefit and either estimated or actual monetary value. |
HarmTypeValues
| Name | Description |
|---|---|
| HarmfulToEnvironment | Impact on natural or semi-natural environments and/or the species they contain. Includes impacts on species, species interactions, habitats, ecosystem composition, functionality and services. |
| HarmfulToLivelihoods | Impact on primary production or subsistence, as well as on safety and social, recreational, aesthetic, spiritual or cultural values. |
| HarmfulToHumanHealth | Impact on human health via disease, allergen, air/water quality, etc. |
EcosystemServicesImpacted Values
| Name | Description |
|---|---|
| Provisioning | Provisioning services, such as food, fibre, fuel, water, biochemicals, natural medicines, pharmaceuticals and ornamental resources. |
| Regulating | Regulating services, i.e. benefits obtained from the regulation of ecosystem processes, such as the regulation of climate, floods, disease, wastes, and water quality. |
| Cultural | Cultural services such as recreation, aesthetic enjoyment and tourism; |
| Supporting | Services that are necessary for the production of all other ecosystem services, such as soil formation, photosynthesis, and nutrient cycling |
*EcosystemServicesImpacted values and descriptions are adapted from: Kettunen, M. & ten Brink, P. 2006. Value of biodiversity- Documenting EU examples where biodiversity loss has led to the loss of ecosystem services. Final report for the European Commission. Institute for European Environmental Policy (IEEP), Brussels, Belgium. 131 pp.
*ImpactStrength values and descriptions are adapted from: Olenin S, Minchin D, Daunys D (2007) Assessment of biopollution in aquatic ecosystems. Marine Pollution Bulletin (Volume 55, Issues 7-9, 2007, Pages 379-394).
*Some ImpactMechanism? values come from the IUCN Red List’s Authority Files.
4. DispersalStatus?
4.1 PROPOSAL: Introduce a DispersalStatus? Concept called MovementStatus?
Status: Investigation
Discussion: DispersalStatus? applies to species movements at all scales – introduction across international borders as well as dispersal from one watershed to the next. We could introduce a DispersalStatus? Concept called MovementStatus? with possible values = Pre-borderMovement and Post-borderMovement.
4.2 PROPOSAL: Introduce Concepts for DispersalMechanisms? and DisperslPathways?
Status: Proposed
Discussion: The problem with the original Cause and Vector concepts is that it would have been difficult for providers to map to values as there are so many. Now they can map to 1 of 3 dispersal mechanisms and/or 1 of 6 dispersl pathways. This simplified approach lends itself to comparative analysis across a wide range of taxa and to policy applications (see the ‘responsibility’ statement in the Descriptions for Pathway values).
4.3 PROPOSAL: Introduce a DateOfFirst? Report concept
Status: Proposed
Discussion: This date is sometimes available when date of introduction is unknown.
4.4 PROPOSAL: Change Method concept to 'Mode' and make it not mandatory
Status: Proposed
4.5 PROPOSAL: What format should we use for dates?
Proposal: Use the TAPIR standard date format
Status: Existing
Discussion: Michael: YYYY-MM-DD is usually unavailable for ‘Date of introduction’. Typically providers have a year or a decade. How do we handle the lack of MM-DD?
Discussion: Michael: You often get pre- or post- a year or a decade. Could we implement something modelled on DAISIE, which uses 2 fields: If the date is precise, the same date appears in both fields. If the first field alone is populated, the meaning = ‘post the date’, if only the second field is populated, the meaning = ‘pre the date’.
Discussion: Jim:We can setup the toolkit to map years (including a decade) to a date field. Mapping multiple columns into a date is more complicated. All databases have standard date fields that can be automatically mapped to the protocol. On this one I think I would suggest we recommend the providers use the SQL standard date fields if at all possible.
DispersalStatuses support the following additional Concepts:
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| DateOfIntroduction | No | String | (undefined) | A textual description of any date (day, month, year, decade, etc.) of introduction |
| DateOfFirstReport | No | String | (undefined) | A textual description of any date (day, month, year, decade, etc.) of first report |
| Mode | No | String | Natural, Deliberate, Accidental, Unknown | A high-level categorization of how the organism is dispersing |
| MovementStatus | No | String | Pre-borderMovement, Post-borderMovement | A high-level classification of where the dispersal is occurring |
| *Mechanism | No | String | Commodity, Vector, NaturalDispersal?, Unknown | Mechanism of arrival, entry and/or dispersal. |
| *Pathway | No | String | Release, Escape, Contaminant, Stowaway, Corridor, Unaided, Unknown | Process that results in the introduction of alien species from one location to another |
| FromCountryCode | No | String | See section 4.4.1.3 | The country the organism is dispersing from |
| Route | No | String | (undefined) | A textual description of the route the organism took from the FromCountryCode?. If used, a LanguageCode? must be specified. |
Mechanism Values
Mechanism of arrival, entry and dispersal
| Name | Description |
|---|---|
| Commodity | Importation of a commodity |
| Vector | Arrival of a transport vector. Vector means the physical means, agent or mechanism which facilitates the transfer of organisms or their propagules from one place to another. |
| NaturalDispersal | Natural spread from a neighbouring region where the species is alien |
Pathways Values
Process that results in the introduction of alien species from one location to another
| Name | Description |
|---|---|
| Release | Intentional introduction as a commodity for release (examples include biocontrol agents, game animals and plants for erosion control - responsibility should be the applicant’s) |
| Escape | Intentional introduction as a commodity but escapes unintentionally (examples include feral crops and livestock, pets, garden plants, live baits - responsibility should be the importer’s) [should this include illegal release of e.g. pets, fish for stocking, biocontrol agents, game animals?] |
| Contaminant | Unintentional introduction with a specific commodity (examples include parasites, pests and commensals of traded plants and animals - responsibility should be the exporter’s) |
| Stowaway | Unintentional introduction attached to or within a transport vector (examples include hull fouling, ballast water/soil/sediment/organisms - responsibility should be the carrier’s) |
| Corridor | Unintentional introduction via human infrastructures linking previously unconnected regions (examples include Lessepsian migrants, Ponto-Caspian aliens in the Baltic- responsibility should be the developer’s) |
| Unaided | Unintentional introduction through natural dispersal of alien species across political borders (potentially all alien taxa are capable of dispersal - responsibility should be the polluter’s) |
*Mechanism and Pathway values and descriptions are adapted from: Hulme PE, Bacher S, Kenis M, Klotz S, Kühn I, Minchin D, Nentwig W, Olenin S, Panov V, Pergl J, Py*ek P, Roques A, Sol D, Solarz W & Vilà, M (2008) Grasping at the routes of biological invasions: a framework to better integrate pathways into policy. Journal of Applied Ecology, 45 (in press).
6. PROPOSAL: Have a Metadata DataModel?.
Status: Investigating
Jim: Does TDWG have something we can use here? The TAPIR MetaData? DataModel? is for the entire data source so it does not fit well.
7. PROPOSAL: Have a Citation DataModel?.
Status: Investigating
Jim: Does TDWG have something we can use here?
8. PROPOSAL: Add GUIDs to each record using LSIDs where appropriate
Status: Proposed
9. PROPOSAL: We need a method to add general text to each record for comments, descriptions, etc.
Status: Proposed
Discussion: Add a “Comments” text field to each DataModel? but insure that the documentation indicates it should not be used for information that is covered in elsewhere in the protocol and cannot be queried at the same level of performance or reliability.
----
Posted Protocol Specification text on Wiki -- AnnieSimpson - 04 Aug 2007
This document defines the protocol that will be used to communicate invasive species data between computers. For information on why the specification includes the features it does, please see the Requirements Specification.
This document is written for individuals who plan on implementing their own GISIN consumer or provider and assumes the reader has some understanding of web service protocols, Hypertext Transfer Protocol (HTTP), Structured Query Language (SQL), and the Global Invasive Species Information Network (GISIN). An Introduction to GISIN is available on this web site. W3 Schools provides a free tutorial on SQL. The protocol specification described here has borrowed from other specifications wherever possible. See the DarwinCore documentation, the OpenGIS Web Map Service (WMS), and Geography Markup Language (GML) for related topics.
A large number of individuals and organizations helped with the initial idea, content, and reviews of this protocol. They include; Jim Graham and Annie Simpson for coordinating and documenting the effort, Jerry Cooper, Bob Morris and Michael Browne for original work on the IASPS documentation which was a starting point for this document; Greg Ruiz and Jim Carlton for their Framework for Vector Science; Pam Fuller, Greg Ruiz, Brian Steves, and Shawn Dalton, for their development of NISBase as the ground breaking work on implementing invasive species data exchange; Michael Browne for facilitating the development of the status categories; Robert Hilliard, Kevin Thiele and Aaron Wilton for assistance in integrating vocabularies, Roger Hyam, Renato De Giovanni, and Markus Doring for help with implementing TAPIR; Donald Hobern and Hannu Saarenmaa for overall guidance, and Liz Sellers, Rob Emery, Jacob Asiedeau, Greg Newman, Catherine Jarnevich, Silvia Ziller, Andrea Grosse, Olivier de Munck, the staff of Invasive Species Specialist Group and the Global Invasive Species Database.
If we have forgotten anyone please let us know!
The protocol has been designed with potential data providers in mind, including, a recognition that these organizations will tend to have simple, flat databases, with minimal technical resources to modify their databases to make them available as a web service. At the same time the protocol must perform at high speeds to allow for both a large number of providers and for providers with very large data sets.
The system operates as an HTTP Request/Response protocol. This is the same method used to serve web pages on the Internet, and ensures, that it can pass through the largest number of firewalls without security problems. This approach also provides the required flexibility with very high performance.
The protocol is a subset of the functionality defined by the TAPIR protocol. Specifically, only simple Key-Value Pair (KVP) requests are supported because complex filters encoded as XML were not required and add significant complexity to the provider software. Within TAPIR, the data type of interest is identified as a "Model" and the data elements within the Model as "Concepts". The protocol described here also implements a limited set of Models and Concepts specifically for the invasive species community. To allow providers to implement the protocol without having to reference the complete TAPIR specification, the present document repeats some of the information that is also available in the TAPIR specification.
The protocol operates by having a client computer submit a request to a specific service on a server computer (also referred to as a the provider). If the server can complete the request it returns the information in a response, otherwise the server returns an error response.
Web services are typically implemented in a web scripting framework such as PHP, ASP, JSP, or CGI with a web scripting language such as PHP, VBScript, JScript, or Perl. Complied languages such as Visual Basic, Java, C# and C++ are also used to program web services.
Each request contains a desired operation and additional parameters depending on which operation is specified.
Operations:
Inventory and Search operations must specify the type of data, or Model, desired. A list of the defined Models for GISIN are below. Types 1 through 3 are supported in version 1.x of the specification.
Models:
Note: We broke out ManagementStatus and ImpactStatus from BioStatus when we realized there could be multiple records for ManagementStatus and/or ImpactStatus for a single BioStatus record (i.e. a single species and location). This allows us to keep the Model records flat.
The form of a request is shown below. "<URL>" is a placeholder for the URL from the registry. The URL must be a fully qualified URL that is available on the Internet. The URL will end with "?" if it contains no parameters and with an "&" if it contains parameters. The additional parameters are added without a delimiter to allow either the first delimiter "?" or a subsequent delimiter "&" to be specified by the provider. Requests can be either GET or POST although POST is recommended.
Request:
http://<URL>Additional Parameters
The Ping, Metadata, and Capabilities operations do not have any additional parameters. Inventory and Search operations include additional parameters to specify the desired data contained to be contained within the response.
a11 25Warning: Because some web services treat parameter names as case sensitive please ensure the letter case of the request matches the specification exactly.
Responses (including errors) are encoded in XML unless images are requested. Images are returned in JPEG, PNG, or GIF formats. Errors are encoded as XML.
Below is a template for a typical response. There are just 2 tags included within a "response" element. The "header" element contains information about the response. The name "operation" in the second element will be replaced by the operation name ("ping", "inventory", etc.). The second element will contain a series of records containing the data of interest.
<?xml version="1.0" encoding="UTF-8"?>
<response>
<header>
<source accesspoint="http://example.org/GISIN.asp"
sendtime="2005-11-11T12:23:56"/>
</header>
<operation>
<record>
<elementName>Element Value</elementName>
</record>
<summary start="0" totalReturned="1"/>
</operation>
</response>
Note: "Contains" is not supported in TAPIR and I have a request for how to perform this without incurring a "COUNT(*)" operation.
Note: "Count" has been replaced by performing an inventory operation with "Count=true" and no Concepts.
Ping is a simple operation that returns a "Pong" from the provider's web service to insure that the service is up and running.
a12 4The Metadata operation returns descriptive information about the web service and the organization hosting it.
Using the inventory command without any Concepts allows the client to determine the number of records that will be available for a given filter. This operation asks the question "How many of a given type of data do you have for a given set of filters?" Examples include:
This operation will return a count of the number of available records given a general format of:
- How many [Model] do you have for [Filter(s)]?
- Returns number of records
A possible SQL statement for this operation is shown below. "COUNT(*)" if the SQL statement to the number of records that match the specified filters. TableName is defined by the desired Model. "RecordSet=Execute(Query)" returns a record set with the first field in the first record equal to the number of records that match the filter. Returning "RecordSet(1)" returns this field.
- Query="SELECT COUNT(*) TableName WHERE Filters"
- RecordSet=Execute(Query)
- Return RecordSet(1)
Note: This operation should be used sparingly since this operation causes the database to search for all the records for a given filter and may be as time consuming as requesting all the actual records for the filter. This operation should not be called each time a block of records is requested, instead call this operation once at the start of a series of requests.
Using the Inventory operation with a list of Concepts allows the client to determine the type and number of records that are available for a given Model and set of filters. Examples include:
This operation will return either a set of records with the specified Concepts and has general form shown below. Concepts indicate the desired content of the response records and how to group the Concepts for counting. ScientificName or Location information is typical. Limit is the maximum number of records the client should return while Start is a zero-referenced index to the first record to return. Model and Filters are the same as defined earlier.
The general form can be translated by the server into a SQL statement of the form below. "DISTINCT" term will limit the result to just the distinct species or locations. Fields will select either the scientific name or the appropriate location fields. The "LIMIT Start, Limit" clause will have the database start at Start and return at most Limit. The server should then return the resulting records encoded as XML.
Limit, Start, Count and Filters are optional.
Search is very similar to Inventory except that it returns individual records instead of grouping them. The operation returns a block of records containing the BioStatuses, ProfileURL, or Occurrence data based on a specified Model and set of Filters. Examples include:
The general form of this operation is shown below. The parameters have been defined in the sections above.
The general form can have the SQL form shown below.
Limit, Start, and Filters are optional.
4.1.1 Ping Example
Request:
http://example.org/service.php?op=Ping
Response:
<?xml version="1.0" encoding="UTF-8"?>
<response>
<header>
<source accesspoint="http://example.org/service.php"
sendtime="2005-11-11T12:23:56"/>
</header>
<pong/>
</response>
The GISIN metadata elements include same elements as TAPIR (t), some of which are derived (dct) from the Dublin Core Metadata Standard (dc):
| Name | Type | Required | Description |
|---|---|---|---|
| <dc:title> | String | Yes | The name or names of the service, which may be in multiple languages (using the xml:lang attribute to identify the language code). |
| <dc:type> | String | Yes | The type of resource according to the Dublin Core Type Vocabulary. This value should be the same for all TAPIR providers: http://purl.org/dc/dcmitype/Service, unless the type vocabulary is refined or changed in the future. The purpose is to indicate that the resource is actually a service. |
| <t:accesspoint> | String | Yes | (synonym of <dc:identifier>). The URL of the service. |
| <dc:description> | String | The description may include, but is not limited to, an abstract, a table of contents, a reference to a graphical representation of content, or a free-text account of the content. Can be provided in different languages. | |
| <dc:language> | String | Yes | The primary language of the data provided by the service. It is recommended to use codes defined by the IANA Language Subtag Registry. |
| <dc:subject> | String | No | Subject and Keywords. Typically, a subject will be expressed as keywords, key phrases or classification codes that describe content provided by the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. |
| <dc:bibliographicCitation> | String | No | Recommended practice is to include sufficient bibliographic detail to identify the resource as unambiguously as possible, whether or not the citation is in a standard form. Can be provided in different languages. |
| <t:rights> | String | No | (homonym of <dc:rights> a statement about property rights) Information about who can access the resource or about its security status, access regulations, etc. Can be provided in different languages. |
| <dct:modified> | Date | No | Date on which the service was last modified |
| <dct:created> | Date | No | Date on which the service was created |
| <t:indexingPreferences> | Element | No | Used to inform data aggregators and indexers about the preferred start time, duration and frequency for performing this operation. Has three attributes: |
| <t:relatedEntity> | Element | Yes | A complex element indicating the entities related to the service. |
| <t:custom> | Element | No | Element of any type to include any additional information that goes beyond the standard TAPIR metadata. |
Please see the TAPIR specification for more information on the Metadata operation, as well as the Dublin Core Metadata Element Set, version 1.1 and the Dublin Core BibliographicCitation.
This function allows the user to determine the types of information (Models) available through a GISIN system provider, and its degree of detail (Concepts).
4.3.1 Capabilities Example
Request:
http://example.org/service.php?op=Capabilities
Response:
<?xml version="1.0" encoding="UTF-8"?>
<response>
<header>
<source accesspoint="http://example.org/service.php"
sendtime="2005-11-11T12:23:56"/>
</header>
<operations>
<ping/>
<metadata/>
<capabilities/>
<inventory>
<template location='http://example.org/InventoryTemplates.html'/>
</inventory>
<search>
<template location='http://example.org/SearchTemplates.html'/>
</search>
</response>
The difference between the inventory and search operations is that the inventory operation aggregates data and the search operation returns data from individual records. The parameters are the same for these operations except that the inventory operation can specify a "count" parameter. Below are the common Concepts and parameters for inventory and search operations that are supported by one or more data Models. The specifics for each data Model follow.
The following Concepts are used to identify the Date, Taxonomy, Location, and the Language for text results within the data for all Models.
| Name | Data Type | Values/Range | Description |
|---|---|---|---|
| DateLastModified | Date | YYYY-MM-DD | See section 4.4.1.1 |
| StartValidDate | Date | YYYY-MM-DD | See section 4.4.1.1 |
| EndValidDate | Date | YYYY-MM-DD | See section 4.4.1.1 |
| Kingdom | String | Monera, Protista, Fungi, Plantae, Animalia | See section 4.4.1.2 |
| ScientificName | String | See section 4.4.1.2 | See section 4.4.1.2 |
| DecimalLatitude | Float | -90 to 90 degrees | See section 4.4.2 |
| DecimalLongitude | Float | -180 to 180 | See section 4.4.2 |
| CountryCode | String | See section 4.4.1.3 | |
| StateName | String | See section 4.4.1.3 | |
| CountyName | String | See section 4.4.1.3 | |
| LocalityName | String | See section 4.4.1.3 | |
| USA_FIPSCode | String | See section 4.4.1.3 | |
| USA_HUC | String | See section 4.4.1.3 | |
| LanguageCode | String | See section 4.4.1.4 |
Note: If a provider does not support a particular Concept it should simply not return that Concept as an element of the record.
Dates are represented as documented in International Standard ISO 8601. This format is YYYY-MM-DD where YYYY is the decimal year in the Gregorian calendar. See Markus's web page for a quick summary. At least a year is required, month and day are preferred as well.
The DateLastModified is the last date that the record was changed. This will be used by data consumers of if they cache data. If the provider does not maintain a DateLastModfiied in their database they should always return the current date.
The StartValidDate and EndValidDate represent the range of when a "status" data Model is valid. Data providers should return an empty element for the EndValidDate if the status is still current.
ScientificName is the primary means of filtering by taxa. At least a Genus is required. Species, subspecies, variety, author, and date may be provided in standard taxonomic notation. Kingdom is recommended to be included in all requests with ScientificName's to resolve the few conflicts where the same genus appears in more than one Kingdom.
Examples of scientific names include:
Note: We need to define how Taxonomic Concepts will be included.
Invasive species location data can be in one of four forms: 1) international codes, 2) locality names, 3) locality codes, and 4) geographic coordinates. International codes exist for countries and are available from the United Nations. Once a country code is specified, locality names can be used within that country. The first subdivision below a country should be province which includes states. The second should be counties (which includes cantons). If names are not associated with a LanguageCode then they are assumed to be in the default language of the provider. Locality codes are defined with a country code as a prefix, e.g. "USA_HUC" for the United States Hydrologic Unit Codes.
| Location Type | Synonyms |
|---|---|
| State | Province, commonwealth |
| County | Shire, canton |
| WaterBody | Lake, stream, river, ocean, sea |
| Locality | City, town, burg,municipality |
| Island | Isle |
Filtering for geographic coordinates is only supported for geographic bounding boxes.
Readers should recognize that certain providers will have only local names while others will have only geographic coordinates (of a variety of types). Consumers may request just LocationNames, just Geographic coordinates, or both. The data provider should provide all the information it has available that meets the requested content.
Languages are specified with IS0 639-2 codes. These are 3-letter codes. In some cases a bibliographic code and a terminology code is provided. In this case GISIN uses the terminology code. Some examples are below.
Below are parameters that can be applied to either Inventory or Search operations and with one or more data Models.
| Name | Data Type | Filter | Description |
|---|---|---|---|
| DateLastModifiedMin | Date | DateLastModified >= Value | Defines the start of the date range for modified records |
| DateLastModifiedMax | Date | DateLastModified <= Value | Defines the end of the date range for modified records |
| ValidDateMin | Date | StartLastModified >= Value | Defines the first date of interest for status reports |
| ValidDateMax | Date | EndLastModified <= Value | Defines the last date of interest for status reports |
| Kingdom | String | Kingdom = Value | Defines the Kingdom of interest |
| ScientificName | String | ScientificName LIKE Value | Defines a complete or partial scientific name |
| DecimalLatitudeMin | Float | DecimalLatitude >= Value | Minium latitude of interest for bounding box or points |
| DecimalLatitudeMax | Float | DecimalLatitude >= Value | Maximum latitude of interest for bounding box or points |
| DecimalLongitudeMin | Float | DecimalLongitude >= Value | Minimum longitude of interest for bounding box or points |
| DecimalLongitudeMax | Float | DecimalLongitude >= Value | Maximum longitude of interest for bounding box or points |
| CountryCode | String | CountryCode = Value | |
| StateName | String | Province LIKE Value | |
| CountyName | String | County LIKE Value | |
| LocalityName | String | Locality LIKE Value | |
| USA_FIPSCode | String | USA_FIPSCode = Value | Federal Information Processing Standard Code (for places, counties, states) |
| USA_HUC | String | USA_HUC = Value | Hydrologic Unit Code |
| LanguageCode | String | LanguageCode = Value | See IS0 639-2 |
| Start | Integer | Record index >=0 | Zero-based index from first record in the record set derived from the specified filters |
| Limit | Integer | Number of records <= Limit | Maximum number of records to return |
| Count | String | Adds a "count" attribute to each record element | |
| Concept | String | Defines w hich fields to return. Multiple Concepts can be specified with multiple Concept parameters. | |
| OrderBy | String | How to order the response data. Multiple "OrderBy" parameters can be specified, e.g. OrderBy=DateLastModified&OrderBy=StateName |
The default operation for the service is to return all the data contained in the service, in other words the default for each filter parameter is the entire valid range.
The BioStatus model contains information on the status of a species within a specific location, and within a specific date range.
BioStatuses are required to support the following general Concepts:
BioStatuses support the following additional Concepts. Possible values for the Concepts are listed below this table.
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| Source | No | String | Citation for the source of the data | |
| Origin | Yes | String | Indigenous, Nonindigenous, Unknown | Whether the species is considered to be native to a particular location or not. |
| Presence | Yes | String | Absent, Sometimes, Present, Unknown | There is supporting evidence to show the species is present within the valid date |
| Persistence | No | String | Persistent, Temporary [let's delete this value. MB], Transient, DiedOut, Unknown | How successful the organism is at surviving and reproducing |
| Distribution | No | String | Widespread, Moderate, Localized, Unknown | Whether the species is limited to a local area or covers vast tracks of land or water |
| Abundance | No | String | Dominant, Common, Rare, Zero, Unknown | How abundant the organism is |
| Trend | No | String | Expanding, Stable, Declining, Unknown | Whether the range of the organism is increasing or decreasing |
| RateOfSpread | No | String | Rapid, Moderate, Slow, Unknown | How quickly the range of the organism is expanding |
| Harmful | Yes | String | Yes, No, Potentially, Unknown | Whether the organism is considered harmful. More detailed 'harm' information is dealt with in the Impact Status element |
| RegulartoryListing | No | String | Prohibited, Restricted, NotConsidered, Unknown | The legal regulatory status of the organism |
Origin Values
| Name | Description |
|---|---|
| Indigenous | Naturally distributed within the region of interest, with a long-term presence extending into the pre-historic record |
| Nonindigenous | (Alien, foreign, exotic, introduced, non-native) Means a species, subspecies, or lower taxon occurring outside of its natural range (past or present) and dispersal potential (i.e. outside the range it occupies naturally or could not occupy without direct or indirect introduction or care by humans) and includes any part, gametes or propagule of such species that might survive and subsequently reproduce (IUCN 2000). Includes aboriginal introductions and archeozoa/archeophytes (early introductions of organisms into Europe by humans that are strongly integrated in European ecosystems) |
| Unknown | Includes 'Cryptogenic' i.e. a species which is neither demonstratively native nor introduced in a region because its origin/native range is unknown, and 'Uncertain' i.e. the native range is known but this occurrence lies somewhere between its known native and nonindigenous ranges. |
Presence Values
| Name | Description |
|---|---|
| Absent | Known to be absent. This may be due to Eradication, Interception at border, Presumed extinct (see Persistence) or Recorded in error. These 'Reasons for absence' may become part of an expanded schema |
| Sometimes present | Vagrant, migratory or an otherwise "casual" presence |
| Present | Known or reported to be present at the date of publication or last update of records. Please note that for aggregated data (e.g. a collection of historic reports), the date of publication or last update of records provides no indication of when the organism was present. |
| Unknown |
Persistence Values
| Name | Description |
|---|---|
| Persistent | Surviving and reproducing in perpetuity. Synonymous with 'naturalized'. |
| Temporary | Surviving and reproducing for a limited period [let's delete this value. MB] |
| Transient | Surviving but not reproducing (e.g. remnant species from old gardens). Synonymous with 'established' |
| Died out | Not surviving. Presumed extinct at the referenced location. |
| Unknown |
Distribution Values
| Name | Description |
|---|---|
| Widespread | Occurs in most of the referenced location. |
| Moderate | Occurs in some but not all parts of the referenced location. |
| Localized | Occurs in only a few parts of the referenced location. |
| Unknown |
Abundance Values
| Name | Description |
|---|---|
| Dominant | Numerically dominant in the referenced location. Depending on the nature of the referenced location, this information could be at the individual, population, community, ecosystem or landscape scale. |
| Common | Common in the referenced location. Moderate abundance |
| Rare | Numerically rare in the referenced location. |
| Zero | Zero abundance means absent. It's ok to have parameters overlap (but not the values within a parameter). |
| Unknown |
Trend Values
| Name | Description |
|---|---|
| Expanding | Biomass is increasing |
| Stable | Zero, or close to zero, trend |
| Declining | Biomass is decreasing |
| Unknown |
RateOfSpread Values
| Name | Description |
|---|---|
| Rapid | |
| Moderate | |
| Slow | |
| Unknown |
Harmful Values
| Name | Description |
|---|---|
| Yes | Any kind of harm has been identified. Could be environmental, social/economic or harmful to human or animal health. |
| No | Benign. Not harmful |
| Potentially | Has been known to be harmful elsewhere or displays tendencies which could become harmful. |
| Unknown |
RegulartoryListing Values
| Name | Description |
|---|---|
| Prohibited | Banned organism |
| Restricted | Organism with some regulatory restriction or control |
| Not considered | Not considered for listing at the date of publication or last update of records |
| Unknown |
BioStatuses are required to support the following general filters:
BioStatuses support the following additional filters:
| Name | Data Type | Returns records with |
|---|---|---|
| Presence | String | Presence = Value |
| Persistence | String | Persistence = Value |
| Distribution | String | Distribution = Value |
| Abundance | String | Abundance = Value |
| Trend | String | Trend = Value |
| RateOfSpread | String | RateOfSpread = Value |
| Harmful | String | Harmful = Value |
| RegulartoryListing | String | RegulartoryListing = Value |
The following example will provide all the BioStatuses within the United States for all species that are both non-native (Native=No) and are considered harmful (this could be considered synonymous with invasive).
Request:
http://example.org/service.php?op=search&Model=BioStatus
&ScientificName=Tamarix&CountryCode=USA&Presence=Present&Harmful=Yes
Response:
<?xml version="1.0" encoding="UTF-8"?>
<response>
<header>
<source accesspoint="http://example.org/GISIN.asp"
sendtime="2005-11-11T12:23:56"/>
</header>
<search>
<record>
<scientificName>Tamarix ramossissima</scientificName>
<countryCode>USA</countryCode>
<presence>Present</presence>
<origin>Indigenous</origin>
<harmful>Yes</harmful>
</record>
<summary start="0" totalReturned="1"/>
</search>
</response>
ProfileURLs are required to support the following general Concepts:
BioStatuses support the following additional Concepts:
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| URL | Yes | String | Fully qualified URL to reach the profile over the Internet |
ProfileURLs can be filtered by the following general filters:
The following example will return all the ProfileURLs available for members of the genus Tamarix.
Request:
http://example.org/service.php?op=search&Model=ProfileURL &ScientificName=Tamarix
Response:
<?xml version="1.0" encoding="UTF-8"?>
<response>
<header>
<source accesspoint="http://example.org/GISIN.asp"
sendtime="2005-11-11T12:23:56"/>
</header>
<search>
<record>
<scientificName>Tamarix ramossissima</scientificName>
<url>http://www.invasivespecies.org?ScientificName=Tamarix ramossissima</url>
</record>
<summary start="0" totalReturned="1"/>
</search>
</response>
Occurrence data are especially important for modeling present and future distributions of species. The GISIN system utilized other TDWG standards in the management of occurrence information.
Occurrences are required to support the following general Concepts:
Occurrences support the following additional Concepts:
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| HorizontalDatum | Yes | String | WGS84, HARN | The Datum used to collection the Latitude and Longitude coordinates |
| StartCollectionDate | Yes | Date | First date when the occurrence data for the record was being collected | |
| EndCollectionDate | Yes | Date | Last date of collections. Typically StartCollectionDate and EndCollectionDate will be the same | |
| Accuracy | No | Float | As close an approximation to the standard deviation of the coordinates expressed in meters. |
The preferred datums are World Geodetic System 1984 (WGS84) or High Accuracy Reference Network (HARN) but providers may have data in datums that are not global and may not have the facilities to convert them to a global datum. Ignoring the datum can cause errors of thousands of meters! We highly encourage providers to provide data in WGS84 or HARN and consumers should always check the datum or else filter to choose just the datums they accept.
Occurrences can be filtered by Taxon, Location, DateLastModified and the following:
| Name | Data Type | Returns records with |
|---|---|---|
| HorizontalDatum | String | HorizontalDatum = Value |
| CollectionDateMin | Date | StartCollectionDate >= Value |
| CollectionDateMax | Date | EndCollectionDate <= Value |
| AccuracyMin | Float | Accuracy >= Value |
| AccuracyMax | Float | Accuracy <= Value |
The following example will provide all the data within the United States where members of the Genus Tamarix are considered non-native and harmful.
Request:
http://example.org/service.php?op=search&Model=BioStatus &ScientificName=Tamarix&CountryCode=USA&Native=No&Harmful=Yes
Response:
<?xml version="1.0" encoding="UTF-8"?>
<response>
<header>
<source accesspoint="http://example.org/GISIN.asp"
sendtime="2005-11-11T12:23:56"/>
</header>
<search>
<record>
<scientificName>Luzula luzuloides</scientificName>
<latitude>40</latitude>
<longitude-105</longitude>
<longitude>Luzula luzuloides</longitude>
<startCollectionDate>10-5-2006</startCollectionDate>
<endCollectionDate>10-5-2006</endCollectionDate>
</record>
<summary start="0" totalReturned="1"/>
</search>
</response>
ImpactStatus represents the type of impact a species is having on a habitat. Multiple ImpactStatues should be provided for species that impact multiple habitats (i.e. marine and terrestrial).
ImpactStatuses are required to support the following general Concepts:
ImpactStatuses support the following additional Concepts:
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| HabitatImpacted | Yes | String | Freshwater, Brackish, Marine, Terrestrial | The habitat being impacted |
| EcosystemImpacted | No | String | Natural, HumanModified | Type of ecosystem being impacted |
| HarmType | No | String | HarmfulToEnvironment, HarmfulToHumanHealth, HarmfulToEconomy | What values the species is impacting |
| ImpactStrength | No | String | Massive, Strong, Moderate, Weak, None, Unknown | How strong the impact is by the species |
HabitatImpacted Values
| Name | Description |
|---|---|
| Freshwater | A primarily freshwater habitat including streams, rivers, and freshwater lakes |
| Brackish | A habitat with a mix of fresh and salt water, typically estuaries but also includes salt marshes and salt lakes |
| Marine | A primarily marine habitat including oceans, seas, and bays |
| Terrestrial | An impact exhibited primarily on land. |
EcosystemImpacted Values
| Name | Description |
|---|---|
| Natural | Few environments are pristine. "Natural" includes semi-natural environments. |
| HumanModified | Includes urban environments as well as ecosystems modified by forestry, agriculture, horticulture, aquaculture, etc. |
HarmType Values
| Name | Description |
|---|---|
| HarmfulToEnvironment | Natural or semi-natural environments and/or the species they contain. Includes, changes to ecosystem functioning and composition, habitat availability, species interactions, hybridization, predation, competition etc. |
| HarmfulToHumanHealth | In the future, expansion may be needed to distinguish between e.g. diseases and allergens. |
| HarmfulToEconomy | Includes livelihood, cultural, medicinal, amenity and social activities |
ImpactStrength Values*
| Name | Description |
|---|---|
| Massive | Causes the extinction of keystone native species, or loss of key habitat, or an extreme ecosystem-wide shift in the food web |
| Strong | Causes population extinctions within the ecosystem, or the alien species is the dominant species, or it causes the alteration of a key habitat, or causes a severe shift in ecosystem functioning within the assessed area |
| Moderate | Causes a large-scales shift in native species abundance, or noticeable changes in type-specific communities, or the alteration and reduction of a habitat; or a moderate modification of an ecosystem’s performance |
| Weak | Causes local displacement of native species but no extinctions, or alteration of a habitat with no change in habitat size, or weak changes in ecosystem function |
| None | Causes no displacement of native species, no habitat alteration, and no change in ecosystem functioning |
| Unknown | The strength of impact is unknown |
*This table is based on: Olenin S, Minchin D, Daunys D (2007) Assessment of biopollution in aquatic ecosystems. Marine Pollution Bulletin (in print).
ImpactStatuses are required to support the following general filters:
ImpactStatuses support the following additional filters:
| Name | Data Type | Returns records with |
|---|---|---|
| Habitat | String | Habitat = Value |
| Ecosystem | String | Ecosystem = Value |
| HarmType | String | HarmType = Value |
| ImpactStrength | String | ImpactStrength = Value |
The following example will provide all the ImpactStatuses within the United States for all records for a species that are having a moderate impact on terrestrial habitats.
Request:
http://example.org/service.php?op=search&Model=ImpactStatus
&ScientificName=Tamarix&CountryCode=USA&Habitat=Terrestrial&ImpactStrength=Moderate
Response:
<?xml version="1.0" encoding="UTF-8"?>
<response>
<header>
<source accesspoint="http://example.org/GISIN.asp"
sendtime="2005-11-11T12:23:56"/>
</header>
<search>
<record>
<scientificName>Euphorbia estula</scientificName>
<countryCode>USA</countryCode>
<habitat>Terrestrial</habitat>
<impactStrength>Present</impactStrength>
</record>
<summary start="0" totalReturned="1"/>
</search>
</response>
DispersalStatus represents the type of Dispersal a species is having on a habitat. Multiple DispersalStatuses should be provided for species that Dispersal multiple habitats (i.e. marine and terrestrial).
DispersalStatuses are required to support the following general Concepts:
DispersalStatuses support the following additional Concepts:
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| DateOfIntroduction | No | String | (undefined) | A textual description of any date (day, month, year, decade, etc.) of introduction |
| Method | Yes | String | Natural, Deliberate, Accidental, Unknown | A high-level categorization of how the organism is dispersing |
| Cause | No | String | See below | The enterprise, activity, trade, endeavor, commerce, motive, rationale, incentive, or reason of accidental (unintentional, inadvertent, escape, chance) or of deliberate (intentional, planned, purposeful, premeditated, planted, direct) dispersal. |
| Vector | No | String | See below | The physical means, agent or mechanism which facilitates the transfer of organisms or their propagules from one place to another. Synonyms = pathway, mode, dispersal mechanism, transport mechanism, manner, carrier, bearer, method. |
| FromCountryCode | No | String | See section 4.4.1.3 | The country the organism is dispersing from |
| Route | No | String | (undefined) | A textual description of the route the organism took from the FromCountryCode. If used, a LanguageCode must be specified. |
Method Values
| Name | Description |
|---|---|
| Natural | Dispersal by an organisms' natural mechanisms and strategies without direct or indirect human intervention |
| Deliberate | Dispersal resulting from intentional human activity |
| Accidental | Unintentional dispersal in association with human activity |
| Unknown |
Cause Values
These represent the reasons that an organism was introduced into an area.
| Name | Description | |
|---|---|---|
| Agriculture | Not horticulture or forestry | |
| Aid | Assistance to humans in disaster situations | |
| AnimalsForaging | Spread by animals seeking food and other resources | |
| Aquaculture | Specifically fresh water | |
| AquariumTrade | Trade in exotic plants or animals for aquariums | |
| BiologicalControl | To biologically control other problematic species (as predators, parasites, etc.) | |
| BotanicalGardens | Collection and public display of exotic plants; does not include horticulture | |
| Breeding | For breeding purposes | |
| ConsumptionExcretion | For example, birds dispersing seeds after they eat fruit | |
| CulturalUse | Includes, e.g., the use of feathers and herbs by traditional cultures | |
| CutFlowerTrade | Commercial trade in cut flowers | |
| Disturbance | A human natural or anthropogenic disturbance which creates the potential for an organism to establish | |
| DuneStabilisation | Exotic plants planted to prevent movement of dunes through wind erosion | |
| ErosionControl | Exotic vegetation planted to prevent soil erosion | |
| EscapeFromConfinement | Escaped from a controlled environment | |
| Flooding | Dispersal in association with sudden or regular (e.g. seasonal) innundation | |
| Food | Food for humans | |
| Forage | Plants used as food for both wild animals and live stock | |
| Forestry | Exotic species planted in forestry, or weeds, pests, or pathogens associated with foresty/logging operations | |
| GardenEscape | Plants or seeds allowed to escape from gardens; not horticulture | |
| GardenWasteDisposal | Organisms spread via garden waste | |
| HarvestingFur | Includes harvesting wool and hair | |
| Hedges | Includes windbreak | |
| Horticulture | Study sites and commercial sites that grow fruits, vegetables, herbs. Not garden escape. Not nursery trade. | |
| IndustrialPurposes | Organisms used for industrial purposes | |
| IntentionalRelease | Includes release for hunting and stocking for fishing | |
| InterconnectedWaterways | Man-made connections of waterways (e.g. canals) that nullify natural geographic barriers | |
| InternetSales | Promotion and trade of exotic organisms via the internet | |
| LandscapeImprovement | flora or fauna "improvement" | |
| LandscapingIndustry | Promotion, import and planting of exotic species by landscaping specialists | |
| LiveFoodTrade | Promotion, import and distribution of live food and/or potential associated contaminants | |
| Mariculture | Marine aquaculture | |
| MedicinalUse | For the treatment of illness | |
| MilitaryActivity | Dispersal associated with military activities | |
| NaturalDisaster | Dispersal as a direct result of natural disaster; not caused by the relief response (see ReliefAid) | |
| NaturalDispersal | The natural dispersal tendencies and strategies of organisms | |
| NurseryTrade | Dispersal, especially of diseases and accidental weeds, caused by nursery trade actvities | |
| OffSitePreservation | Dispersal associated with conservation activities | |
| OrnamentalPurposes | Decorative plants and animals dispersed for ornamental purposes | |
| Other | ||
| OtherRecreational | Dispersal as people move through natural landscapes or aquatic environments for outdoor recreational activities such as tramping, off-road vehicles, boating or yachting, hunting, fishing (Does not include intentional release of animals) | |
| PeopleForaging | Spread by people seeking resources | |
| PeopleSharingResources | Example include the exchange of seed, livestock or water from contaminated sources | |
| PetTrade | Trade in exotic animals as pets | |
| ReliefAid | Assistance to humans or livestock in disaster situations | |
| Research | The introduction of exotic specimens for scientific research | |
| SeedTrade | Dispersal in association with the exotic seed trade | |
| Smuggling | Intentional illegal introduction for profit | |
| TimberTrade | Sawn timber (not logs) can be contaminated with pests and pathogens | |
| VegetativeGrowth | Natural plant propagation including reproduction by root suckers and regeneration from rhizome fragments | |
| WormCultivation | Dispersal in association with worm cultivation | |
| Zoos | The collection of exotic animal specimens |
Vector Values
These values represent the mechanism the organism is using to disperse. The values are listed alphabeticallyin the table below but can be categoried into the following groups for reference:
Vehicles:
Item that carried the organism:
Free movement:
Freight:
Other:
| Name | Description |
|---|---|
| Aircraft | The aircraft itself. This does not include airfreight, passengers or crew |
| AirFreight | Brought in by aircraft as freight |
| AnimalCaptive | Pets, animals for agri/mari/aqua/culture, fur trade, hunting, fishing, zoo, biocontrol, etc. |
| AnimalFree | Naturally occurring or introduced animals |
| BulkFreight | Includes timber, soil, sand, tyres, rubbish, etc. Does not include airfreight |
| Container | Shipping container (loaded or empty) used for land, sea or air transport |
| FloatingDebris | Includes vegetation |
| FreshAnimalProduct | Includes bait |
| FreshProduce | Fresh fruit and vegetables |
| FloatingDebris | Includes vegetation |
| GeneralFreight | Includes machinery, products and household goods. |
| GermPlasm | Includes specimens, plants, animals, bacteria, etc. |
| Human | Includes passengers, crew, tourists, and their souvenirs, clothing, equipment and footware. |
| LandTransportVehicle | The vehicle itself - motorised or non-motorised. Includes trailers and machinery, gear, etc. |
| ManufacturedAnimalFeed | Does not include pure plant feed such as grain, hay or straw. |
| Other | |
| OtherConsumable | Honey, dried meat, live (sea)food etc. |
| Packaging | Includes solid wood packing material such as pallets |
| PlantMaterial | Vegatation or seeds. Not produce or germplasm. Includes cut flowers, plant stock and habitat material, garden waste, mulch, straw |
| Postal | Postal or courier item |
| Ship | The ship/boat itself. Includes hull, superstructure, gear, ballast and bilge water |
| Water | Floating on or in the water |
| Wind | Floating or flying on the wind |
DispersalStatuses are required to support the following general filters:
DispersalStatuses support the following additional filters:
| Name | Data Type | Returns records with |
|---|---|---|
| Method | String | Method = Value |
| Cause | String | Cause = Value |
| Vector | String | Vector = Value |
| FromCountryCode | Integer | CountryCode = Value |
The following example will provide all the DispersalStatuses within the United States for all species that are naturally dispersing.
Request:
http://example.org/service.php?op=search&Model=DispersalStatus
&CountryCode=USA&Method=Natural
Response:
<?xml version="1.0" encoding="UTF-8"?>
<response>
<header>
<source accesspoint="http://example.org/GISIN.asp"
sendtime="2005-11-11T12:23:56"/>
</header>
<search>
<record>
<scientificName>Euphorbia estula</scientificName>
<countryCode>USA</countryCode>
<method>Natural</method></record>
<summary start="0" totalReturned="1"/>
</search>
</response>
ManagementStatus represents the type of management activities involved with a species in a specified area. Multiple ManagementStatues should be provided for if multiple activities are engaged in the same time period.
ManagementStatuses are required to support the following general Concepts:
ManagementStatuses support the following additional Concepts:
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| Action | Yes | String | Prevention, Eradication, Control, Containment, Mitigation, Interception | The action taken by management |
| Status | No | String | Proposed, Executing, Completed, Unknown | The current status of the specified action |
Action Values
| Name | Description |
|---|---|
| Prevention | Measures taken to stop a species from entering an area. |
| Eradication | Actions taken that eliminate all occurrences of a species |
| Control | Measures taken to reduce a species’ biomass |
| Containment | Measures taken to keep a species within a defined area |
| Mitigation | Actions taken to reduce the harmful effects of a species |
| Interception | Detection of a species at a border and prevention of its entering an area. |
Status Values
| Name | Description |
|---|---|
| Proposed | Includes even the suggestion that the activity would be a good idea, because this indicates concern about the organism |
| Executing | Includes e.g. prevention systems in place and/or public education |
| Completed | Prevention projects are usually ongoing, completed implies no further control effort. |
ManagementStatuses are required to support the following general filters:
ManagementStatuses support the following additional filters:
| Name | Data Type | Returns records with |
|---|---|---|
| Habitat | String | Habitat = Value |
| Ecosystem | String | Ecosystem = Value |
| ManagementType | String | ManagementType = Value |
| ManagementStrength | String | ManagementStrength = Value |
The following example will provide all the ManagementStatuses within the United States for all species that have records of being eradicated.
Request:
http://example.org/service.php?op=search&Model=ManagementStatus
&Type=Eradication
Response:
<?xml version="1.0" encoding="UTF-8"?>
<response>
<header>
<source accesspoint="http://example.org/GISIN.asp"
sendtime="2005-11-11T12:23:56"/>
</header>
<search>
<record>
<scientificName>Euphorbia estula</scientificName>
<countryCode>USA</countryCode>
<habitat>Terrestrial</habitat>
<type>Eradication</type>
</record>
<summary start="0" totalReturned="1"/>
</search>
</response>
Errors are returned in an XML response as shown below. The content of the "error" element should be an error that is appropriate for end-users. This should include information on what happened in end-user terminology and enough information for them to know what they should do next. Additional information for technical users to know how to resolve the problem should also be included.
<?xml version="1.0" encoding="UTF-8"?>
<response>
<header>
<source accesspoint="http://example.org/GISIN.asp"
sendtime="2005-11-11T12:23:56"/>
</header>
<error>
Sorry, there is a technical problem and our staff has been notified.
Please try again tomorrow.
</error>
</response>
Carlton, J.T. and G.M. Ruiz. 2002. Principles of Vector Science and Integrated Vector Management. In Mooney, H. et al. (eds.) Best Practices for the Prevention and Management of Alien Invasive Species. Island Press
IUCN 2000. Guidelines for the prevention of biodiversity loss due to biological invasion. IUCN – The World Conservation Union, Gland, Switzerland
1. Do we specify taxonomic hierarchy or just kingdom/scientific name
- Just kingdom/scientific name for now
2.Can ask service: do you supported hierarchical taxon queries?
- Later addition
3. Need a method to determine if a record is from its original data set or is a duplicate
4. Need a method to determine the original source of a duplicated record
5. Need to include LSIDs for each record. Will LSIDs address issues 3 and 4?
6. The Metadata in TAPIR uses' 2 letter language codes. Should we do the same?
1. PROPOSAL: Add a new data model for EnvironmentalInfo
Status: Proposed
This datamodel will help distinguish between species that occur in natural or human modified environments, and/or in freshwater, brackish, marine and terrestrial habitats. Multiple values are possible. These concepts are different from EcosystemImpacted and HabitatImpacted (a terrestrial species can impact aquatic environments). At the GISIN portal someone could filter by ‘terrestrial‘ to get all terrestrial species – whether or not the habitat impacted might be both terrestrial and aquatic.
EnvironmentalInfo supports the following additional Concepts: Possible values for the additional Concepts are listed in the table.
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| SpeciesEnvironment | No | String | Natural, HumanModified | The environment in which the species occurs |
| SpeciesHabitat | No | String | Freshwater, Brackish, Marine, Terrestrial | The habitat in which the species occurs |
2. PROPOSAL: Change Harmful back to Invasive in BioStatus
Status: Proposed
Discussion: Many believe that ‘Harm’ is subjective and that it is the culmination of the invasion process, which begins with establishment, then persistence and spread. If we provided the word ‘Invasive’ instead of ‘Harmful’ in the BioStatus concept, most providers would be able to map to its possible values, but each provider might mean something different. The key differences are between;
1. Scientific uses of the word ‘Invasive’ meaning ability to spread (i.e. Distribution = Widespread or Moderate, and/or Abundance= Dominant or Common) and
2. Policy uses of the word ‘Invasive’ meaning ability to cause harm.
Different meanings or usages can be deduced from the additional concepts for which data is provided. Currently, the first group can select ‘Invasive’ then map their data to Distribution = (Widespread or Moderate), and/or Abundance= (Dominant or Common) and/or Harmful= (Yes or Potentially).
The second group can select ‘Invasive’ then map their data to ImpactStatus concepts as well as those of group 1.
More Discussion: Folks had major issues with the term “Invasive”. We decided to use “Harmful=Yes”. However, invasiveness data would not be mapped to the ‘Harmful’ concept if there is only evidence of establishment, persistence and spread (e.g. when harm has not been confirmed). A search at the GISIN portal on Harmful = yes would miss this invasiveness data.
BioStatuses support the following additional Concepts. Possible values for the Concepts are listed below this table.
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| Source | No | String | Citation for the source of the data | |
| Origin | Yes | String | Indigenous, Nonindigenous, Unknown | Whether the species is considered to be native to a particular location or not. |
| Presence | Yes | String | Absent, Sometimes, Present, Unknown | There is supporting evidence to show the species is present within the valid date |
| Persistence | No | String | Persistent, Temporary [let's delete this value. MB], Transient, DiedOut, Unknown | How successful the organism is at surviving and reproducing |
| Distribution | No | String | Widespread, Moderate, Localized, Unknown | Whether the species is limited to a local area or covers vast tracks of land or water |
| Abundance | No | String | Dominant, Common, Rare, Zero, Unknown | How abundant the organism is |
| Trend | No | String | Expanding, Stable, Declining, Unknown | Whether the range of the organism is increasing or decreasing |
| RateOfSpread | No | String | Rapid, Moderate, Slow, Unknown | How quickly the range of the organism is expanding |
| Invasive | Yes | String | Yes, No, Potentially, Unknown | Whether the organism is considered invasive. 'Spread' information is dealt with here. 'Harm' information in the ImpactStatus element |
| RegulartoryListing | No | String | Prohibited, Restricted, NotConsidered, Unknown | The legal regulatory status of the organism |
3. ImpactStatus
3.1 PROPOSAL: Introduce an ImpactMechanism concept
Status: Proposed
Introduce an ImpactMechanism concept to handle information about competition, predation, etc. i.e. how IAS damage species habitats and ecosystems. This kind of information is widely available and ImpactMechanism allows us to make assumptions about which kinds of native species may be threatened.
3.2 PROPOSAL: Change HarmType values from HarmfulToEconomy to HarmfulToLivelihoods.
Status: Proposed
3.3 PROPOSAL: Make HabitatImpacted non-mandatory
Status: Proposed
ImpactStatuses support the following additional Concepts:
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| HabitatImpacted | No | String | Freshwater, Brackish, Marine, Terrestrial | The habitat being impacted |
| EcosystemImpacted | No | String | Natural, HumanModified | Type of ecosystem being impacted |
| HarmType | No | String | HarmfulToEnvironment, HarmfulToHumanHealth, HarmfulToLivelihoods | What values the species is impacting |
| ImpactMechanism | No | String | Allergenic, Competition, DiseaseTransmission, Herbivory, Hybridisation, InteractionWithOtherInvasiveSpecies, Pathogenic/Parasite, PhysicalDisturbance, Predation, SoilTransformation, Transpiration, Other, Unknown | Mechanism by which negative impacts occur |
| *ImpactStrength | No | String | Massive, Strong, Moderate, Weak, None, Unknown | How strong the impact is |
4. DispersalStatus
4.1 PROPOSAL: Introduce a DispersalStatus Concept called MovementStatus
Status: Investigation
Discussion: DispersalStatus applies to species movements at all scales – introduction across international borders as well as dispersal from one watershed to the next. We could introduce a DispersalStatus Concept called MovementStatus with possible values = Pre-borderMovement and Post-borderMovement.
4.2 PROPOSAL: Introduce Concepts for DispersalMechanisms and DisperslPathways
Status: Proposed
Discussion: The problem with the original Cause and Vector concepts is that it would have been difficult for providers to map to values as there are so many. Now they can map to 1 of 3 dispersal mechanisms and/or 1 of 6 dispersl pathways. This simplified approach lends itself to comparative analysis across a wide range of taxa and to policy applications (see the ‘responsibility’ statement in the Descriptions for Pathway values).
4.3 PROPOSAL: Introduce a DateOfFirst Report concept
Status: Proposed
Discussion: This date is sometimes available when date of introduction is unknown.
4.4 PROPOSAL: Change Method concept to 'Mode' and make it not mandatory
Status: Proposed
4.5 PROPOSAL: What format should we use for dates?
Proposal: Use the TAPIR standard date format
Status: Existing
Discussion: Michael: YYYY-MM-DD is usually unavailable for ‘Date of introduction’. Typically providers have a year or a decade. How do we handle the lack of MM-DD?
Discussion: Michael: You often get pre- or post- a year or a decade. Could we implement something modelled on DAISIE, which uses 2 fields: If the date is precise, the same date appears in both fields. If the first field alone is populated, the meaning = ‘post the date’, if only the second field is populated, the meaning = ‘pre the date’.
Discussion: Jim:We can setup the toolkit to map years (including a decade) to a date field. Mapping multiple columns into a date is more complicated. All databases have standard date fields that can be automatically mapped to the protocol. On this one I think I would suggest we recommend the providers use the SQL standard date fields if at all possible.
DispersalStatuses support the following additional Concepts:
| Concept | Required | Type | Values | Description |
|---|---|---|---|---|
| DateOfIntroduction | No | String | (undefined) | A textual description of any date (day, month, year, decade, etc.) of introduction |
| DateOfFirstReport | No | String | (undefined) | A textual description of any date (day, month, year, decade, etc.) of first report |
| Mode | No | String | Natural, Deliberate, Accidental, Unknown | A high-level categorization of how the organism is dispersing |
| MovementStatus | No | String | Pre-borderMovement, Post-borderMovement | A high-level categorization of how the organism is dispersing |
| *Mechanism | No | String | Commodity, Vector, NaturalDispersal, Unknown | Mechanism of arrival, entry and/or dispersal. |
| *Pathway | No | String | Release, Escape, Contaminant, Stowaway, Corridor, Unaided, Unknown | Process that results in the introduction of alien species from one location to another |
| FromCountryCode | No | String | See section 4.4.1.3 | The country the organism is dispersing from |
| Route | No | String | (undefined) | A textual description of the route the organism took from the FromCountryCode. If used, a LanguageCode must be specified. |
Mechanism Values
Mechanism of arrival, entry and dispersal
| Name | Description |
|---|---|
| Commodity | Importation of a commodity |
| Vector | Arrival of a transport vector. Vector means the physical means, agent or mechanism which facilitates the transfer of organisms or their propagules from one place to another. |
| NaturalDispersal | Natural spread from a neighbouring region where the species is alien |
Pathways Values
Process that results in the introduction of alien species from one location to another
| Name | Description |
|---|---|
| Release | Intentional introduction as a commodity for release (examples include biocontrol agents, game animals and plants for erosion control - responsibility should be the applicant’s) |
| Escape | Intentional introduction as a commodity but escapes unintentionally (examples include feral crops and livestock, pets, garden plants, live baits - responsibility should be the importer’s) [should this include illegal release of e.g. pets, fish for stocking, biocontrol agents, game animals?] |
| Contaminant | Unintentional introduction with a specific commodity (examples include parasites, pests and commensals of traded plants and animals - responsibility should be the exporter’s) |
| Stowaway | Unintentional introduction attached to or within a transport vector (examples include hull fouling, ballast water/soil/sediment/organisms - responsibility should be the carrier’s) |
| Corridor | Unintentional introduction via human infrastructures linking previously unconnected regions (examples include Lessepsian migrants, Ponto-Caspian aliens in the Baltic- responsibility should be the developer’s) |
| Unaided | Unintentional introduction through natural dispersal of alien species across political borders (potentially all alien taxa are capable of dispersal - responsibility should be the polluter’s) |
6. PROPOSAL: Have a Metadata DataModel.
Status: Investigating
Jim: Does TDWG have something we can use here? The TAPIR MetaData DataModel is for the entire data source so it does not fit well.
7. PROPOSAL: Have a Citation DataModel.
Status: Investigating
Jim: Does TDWG have something we can use here?
8. PROPOSAL: Add GUIDs to each record using LSIDs where appropriate
Status: Proposed
9. PROPOSAL: We need a method to add general text to each record for comments, descriptions, etc.
Status: Proposed
Discussion: Add a “Comments” text field to each DataModel but insure that the documentation indicates it should not be used for information that is covered in elsewhere in the protocol and cannot be queried at the same level of performance or reliability.
-- Main.AnnieSimpson - 04 Aug 2007 added DateOfIntroduction into Table 4.4.7; added detailed descriptions for 'cause' and 'vector'; added detailed scriptio -- Main.AnnieSimpson - 05 Aug 2007 Added ImpactStrength values (and reference) to table at end of section 4.4.6.1. -- Main.AnnieSimpson - 06 Aug 2007 Removed AbundanceValue = monoculture -- Main.AnnieSimpson - 09 Aug 2007 @ 1.10 log @none @ text @d1 1 a1 1 %META:TOPICINFO{author="MichaelBrowne" date="1194484376" format="1.1" version="1.10"}% d2119 347 d2497 1 a2497 1 -- Main.AnnieSimpson - 09 Aug 2007@ 1.9 log @none @ text @d1 1 a1 1 %META:TOPICINFO{author="MichaelBrowne" date="1194479295" format="1.1" version="1.9"}% d3 1 a3 1 persistence d1257 1 a1257 1
Habitat Values
d1308 1 a1308 1Ecosystem Values
@ 1.8 log @none @ text @d1 1 a1 1 %META:TOPICINFO{author="MichaelBrowne" date="1193532814" format="1.1" version="1.8"}% d3 1 a3 1 d712 1 a712 1ImpactStrength Values
d1354 1 a1354 1Note: we need more quantifiable terms here
d2148 4 a2151 1 -- Main.AnnieSimpson - 05 Aug 2007@ 1.3 log @none @ text @d1 1 a1 1 %META:TOPICINFO{author="AnnieSimpson" date="1186286086" format="1.1" reprev="1.3" version="1.3"}% d15 2 a16 2