Association for Pathology Informatics 1/27/03
Tissue MicroArray Common Data Elements

histo

   Identifier: histo
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: en
   Obligation: Required
   Datatype: Empty
   Maximum Occurrence: One
   Definition: Root element of the Tissue Microarray document
   Comment:


header
   Identifier: header
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Required
   Datatype: Empty
   Maximum Occurrence: Unlimited
   Definition: Ancestor element for dublin core header elements
   Comment:


Title
   Identifier: Title
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: A name given to the resource.
   Comment: Typically, a Title will be a name by which the resource is
   formally known.


Creator
   Identifier: Creator
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: An entity primarily responsible for making the content
   of the resource.
   Comment: Examples of a Creator include a person, an organisation,
   or a service. Typically, the name of a Creator should be used to
   indicate the entity.


Subject and Keywords
   Identifier: Subject
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: The topic of the content of the resource.
   Comment: Typically, a Subject will be expressed as keywords, key
   phrases or classification codes that describe a topic of the resource.
   Recommended best practice is to select a value from a
   controlled vocabulary or formal classification scheme.


Description
   Identifier: Description
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: An account of the content of the resource.
   Comment: Description may include but is not limited to: an abstract,
   table of contents, reference to a graphical representation of content
   or a free-text account of the content.


Publisher
   Identifier: Publisher
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: An entity responsible for making the resource available
   Comment: Examples of a Publisher include a person, an organisation,
   or a service. Typically, the name of a Publisher should be used to
   indicate the entity.


Contributor
   Identifier: Contributor
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: An entity responsible for making contributions to the
   content of the resource.
   Comment: Examples of a Contributor include a person, an organisation,
   or a service. Typically, the name of a Contributor should be used
   to indicate the entity.


Date
   Identifier: Date
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: A date associated with an event in the life cycle of the
   resource.
   Comment: Typically, Date will be associated with the creation or
   availability of the resource.  Recommended best practice for encoding
   the date value is defined in a profile of ISO 8601
   [W3CDTF] and follows the YYYY-MM-DD format.


Resource Type
   Identifier: Type
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: The nature or genre of the content of the resource.
   Comment: Type includes terms describing general categories, functions,
   genres, or aggregation levels for content. Recommended best practice
   is to select a value from a controlled vocabulary
   (for example, the working draft list of Dublin Core Types [DCT1]).
   To describe the physical or digital manifestation of the resource,
   use the FORMAT element.


Format
   Identifier: Format
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: The physical or digital manifestation of the resource.
   Comment: Typically, Format may include the media-type or dimensions
   of the resource. Format may be used to determine the software,
   hardware or other equipment needed to display or operate their source.
   Examples of dimensions include size and duration. Recommended best
   practice is to select a value from a controlled vocabulary
   (for example, the list of Internet Media Types [MIME] defining
   computer media formats).


Resource Identifier
   Identifier: Identifier
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: An unambiguous reference to the resource within a given
   context.
   Comment: Recommended best practice is to identify the resource by
   means of a string or number conforming to a formal identification
   system. Example formal identification systems include the Uniform
   Resource Identifier (URI) (including the Uniform Resource Locator
   (URL)), the Digital Object Identifier (DOI) and the International
   Standard Book Number (ISBN).


Source
   Identifier: Source
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: A Reference to a resource from which the present resource
   is derived.  Comment: The present resource may be derived from the
   Source resource in whole or in part.  Recommended best practice is
   to reference the resource by means of a string or number
   conforming to a formal identification system.


Language
   Identifier: Language
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: A language of the intellectual content of the resource.
   Comment: Recommended best practice for the values of the Language
   element is defined by RFC 1766 [RFC1766] which includes a two-letter
   Language Code (taken from the ISO 639 standard [ISO639]), followed
   optionally, by a two-letter Country Code (taken from the ISO 3166
   standard [ISO3166]). For example, 'en' for English, 'fr' for French,
   or 'en-uk' for English used in the United Kingdom.


Relation
   Identifier: Relation
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: A reference to a related resource.
   Comment: Recommended best practice is to reference the resource
   by means of a string or number conforming to a formal identification
   system.


Coverage
   Identifier: Coverage
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: The extent or scope of the content of the resource.
   Comment: Coverage will typically include spatial location (a place name or geographic
   coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a
   named administrative entity). Recommended best practice is to select a value from a controlled
   vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where
   appropriate, named places or time periods be used in preference to numeric identifiers such as
   sets of coordinates or date ranges.


Rights Management
   Identifier: Rights
   Version: 1.1
   Registration Authority: Dublin Core Metadata Initiative
   Language: en
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: Information about rights held in and over the resource.
   Comment: Typically, a Rights element will contain a rights management statement for the
   resource, or reference a service providing such information. Rights information often
   encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the
   Rights element is absent, no assumptions can be made about the status of these and other rights
   with respect to the resource.


filename
   Identifier: filename
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: One
   Definition: This is the name of the document file
   Comment:


tma
   Identifier: tma
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Required
   Datatype: Empty
   Maximum Occurrence: Unlimited
   Definition: Ancestor element for block and header elements.
   Comment: This tag is necessary, because the file could, in theory,
   contain more than one tma data set, and you'd need to keep them
   apart in that case.  You don't need an identifier for each tma,
   though, because a tma is identified by its block.


block
   Identifier: block
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Required
   Datatype: Empty
   Maximum Occurrence: Unlimited
   Definition: Ancestor element for block, core and slide elements
   Comment:


block_purpose
   Identifier: block_purpose
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character string
   Maximum Occurrence: Unlimited
   Definition: A statement on the type of block, such as
   "Prostate cancer progression array."
   Comment: The purpose is to explain the purpose or the intended use of
   the block


block_identifier
   Identifier: block_identifier
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is the block identifier created at the laboratory
   where the TMA block was assembled.  This can take on the identifying
   scheme of the submitting laboratory and should be submitted as a text
   string.
   Comment:


block_description
   Identifier: block_description
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is a text field with a description of the type of TMA block it is, e.g. prostrate
   cancer block.  There is no control over this field and a creator may describe the block as they
   please.
   Comment: This is a good element to include your key words.


block_meshnumbers
   Identifier: block_meshnumbers
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is a text that conveys any mesh numbers with our
   without corresponding mesh terms, that the creator my choose to
   describe the block.
   Comment: These numbers could be used for indexing purposes. This is a
   good element in which to include key words along with their mesh numbers,
   for the benefit of indexers that look for mesh numbers.  A suggested
   way to show data in this element is:
   adenoma|C04.557.470.035, intestine|A03.492.411,
   large intestine|A03.492.411.495, polyp|C04.799


block_related-blocks
   Identifier: block_related-blocks
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This gives the local laboratory TMA block_id’s for other tissue microarray blocks
   that contain tissue from the same of any of the donor block surgical pathology cases, i.e. any
   other block that has a core that was taken from the same surgical pathology block  as a core in
   this block.
   Comment:


block_creator
   Identifier: block_creator
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is a local identifier for the person who assembled, i.e. manufactured as opposed
   to designed, the TMA block; input as Last Name, First Name, Middle Initial.
   Comment:


block_creation-date
   Identifier: block_creation-date
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Date (YYYY-MM-DD)
   Maximum Occurrence: Unlimited
   Definition: This is the date that the TMA block was manufactured.  It should be entered as
   integers in the following format: YYYY-MM-DD, e.g. 1999-05-01.
   Comment: Modifications to an existing block should be treated as “newly created” blocks that
   share cores with other TMA blocks (see block_related_blocks)


block_protocol
   Identifier: block_protocol
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character StringMaximum Occurrence: Unlimited
   Definition: This is the protocol used to manufacture the TMA block, e.g. automated vs. manual,
   low or high melt paraffin-may be a pointer to a URI  or file of protocols.
   Comment: At this time, there is no particular list of  terms used to descirbe the protocol.


block_number-of-cores
   Identifier: block_number-of-cores
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Integer
   Maximum Occurrence: Unlimited
   Definition: This is the total number of cores on the TMA block; input as an integer.
   Comment: Can range from 1 to infinity.  A regular surgical pathology block, with one piece of
   tissue, could be represented as a TMA


block_core-size
   Identifier: block_core-size
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Real Number
   Maximum Occurrence: Unlimited
   Definition: This is the diameter of an individual core in millimeters (mm); a single value per
   block is assumed expressed as a real number with one decimal place, e.g. 0.6 mm.
   Comment:


block_core-spacing
   Identifier: block_core-spacing
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Real Numbers
   Maximum Occurrence: Unlimited
   Definition: This are the spacings between cores in the TMA block express in millimeters (mm);
   this may be a single value or a series of numbers each should be expressed as a decimal number
   with one decimal place, e.g. 3.5 mm.
   Comment:


block_qa
   Identifier: block_qa
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: A free-text description of Quality Assurance procedures performed on the block,
   including a listing of the slide numbers (cut section numbers on the block) for which the QA had
   been performed.
   Comment: This element can contain a great deal of text. It can also contain, instead of lengthy
   text,  a URI that contains the text document that describes the QA procedure for the block.


block_status
   Identifier: block_status
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This element gives the current status if known for the block; it can have one of three
   values: Production, Retired, Exhausted, or Unknown.
   Comment:  Controlled Value


block_array-hash
   Identifier: block_array-hash
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is a hashed array that associates an identifier
   with a core location in the block (key-value pair).  For example,
   a 1000 core TMA may have an array that consists of keys ranging from
   1 to 1000 and key-values each representing the  x,y location for each
   core in the block array.
   Comment: Manufacturers can either omit this element or include the
   element in an encrypted form to protect their intellectucal
   property.


slide
   Identifier: slide
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Required
   Datatype: Empty
   Maximum Occurrence: Unlimited
   Definition: Ancestor element for slide elements
   Comment:


slide_identifier
   Identifier: slide_identifier
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is the slide identifier issued by the distributor; it is a an character string that
   permits the following characters “[0-9][a-z][A-Z].-_: “
   Comment: It may be wise to include something that specifically identifies the institution in the
   identifier, such as JHU-TMA-749839003-1


slide_cut-date
   Identifier: slide_cut-date
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Date (YYYY-MM-DD)
   Maximum Occurrence: Unlimited
   Definition: This is the date that the slide was cut; it should be expressed in integers as YYYY-
   MM-DD
   Comment:


slide_storage
   Identifier: slide_storage
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: unlimited
   Definition: This parameter defines the storage conditions for the slides once they were cut and
   prior to staining.
   Comment: We expect that most users will use something like: regular paraffin sections, room
   temperature; Liquid nitrogen, -70 degrees Centigrade, paraffin-encased slides, 4 degrees
   Centigrade. If the storage protocol is not widely used, it would be wise to include a URI where
   the storage protocol may be found.


slide_section-thickness
   Identifier: slide_section-thickness
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Integer
   Maximum Occurrence: Unlimited
   Definition: This is the thickness of the section expressed as an real number in microns
   Comment:


slide_level
   Identifier: slide_level
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Integer
   Maximum Occurrence: Unlimited
   Definition: This is an integer corresponding to the level of the block for this slide, e.g. 25.
   Comment: Some people may include the level number in the slide_identifier element (as a
   suffix).  If this is the case, they should either redundantly include the suffix in this element or
   describe how the level may be extracted from the slide_identifier in the
   block_protocol element.


slide_sectioning-protocol
   Identifier: slide_sectioning-protocol
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This gives the protocol for sectioning, e.g. tape, no tape, a free-text protocol
   description or a URI where there sectioning protocol is described.


slide_test-date
   Identifier: slide_test-date
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Date (YYYY-MM-DD)
   Maximum Occurrence: Unlimited
   Definition: This is the date that the slide was stained; it should
   be expressed in integers as YYYY-MM-DD.
   Comment:


slide_test-category
   Identifier: slide_test-category
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is the type of special study applied to this slide, e.g. FISH,
   Immunohistochemistry, in situ PCR, BLOT, regular stain, other.
   Comment: This is a controlled vocabulary. Presumably we will be adding additional vocabulary
   terms to this data element.  If you use "other", then you should probably
   be sure that you give a complete description of the protocol in the
   slide_test_protocol element.


slide_test-protocol
   Identifier: slide_test-protocol
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is the description of the slide test protocol,
   e.g. for IH it would describe antigen retrieval (if any), use of
   blocking antibody, staining method, signal, clone and titer used,
   known specificity, epitope chromophore, and link to manufacturer
   information if available; for FISH include test and reference  probe
   labels and links to manufacturer if available; this input may be
   an uncontrolled text string, a pointer to a table in a database,
   or a URI.
   Comment: Attributes are optionally available for this element
      Attribute: name is probe_type and allowed values are "fish" "ih" "other"
      Attribute: name is agent and allowed values are any character string
      Attribute: name is protocol and allowed values are character strings representing URIs


slide_stain
   Identifier: slide_stain
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This element uses a controlled vocabulary for immuno ab for immunohistochemical
   antibody stain immuno in situ for immunohistochemical in situ stain FISH for fluorescence in
   situ hybridization stain.
   Comment: Controlled Value


slide_test-control
   Identifier: slide_test-control
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This Character input is controlled; it gives the quality control review of the test
   performed on the slide e.g. positive and negative control for IH, reference probe for FISH, and
   should take on the value of either “Adequate” or “Not Adequate” or “No QA”.
   Comment:


core
   Identifier: core
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Required
   Datatype: Empty
   Maximum Occurrence: Unlimited
   Definition: Ancestor element for cores
   Comment:


core_array-id
   Identifier: core_array-id
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is the text string core identifier and is an
   element of the array of core identifiers in block_array_hash.
   Comment:


core_tissue-fixative
   Identifier: core_tissue-fixative
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: Text string defining the fixative solution used to fix the tissue in the donor block,
   specifically Alcohol, Bouin's, Hartmann's, Formalin, B5, Other Specify
   Comment: An attribute is optionally available for this element
   Attribute: name is preparation and allowed values are "frozen" "not_frozen"


core_organism
   Identifier: core_organism
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String representing taxonomy.dat identifier number
   followed by an allowable taxonomy.dat name for the identifier number
   Maximum Occurrence: Unlimited
   Definition: Organism name at species level for organism whose tissue
   is represented in the donor block,
   Comment: URI for taxonomy.dat is ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat
   The correct entry for human tissue is "9606 human"


core_demographics-record
   Identifier: core_demographics-record
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: A pointer to a URI where the demographic record is held
   Comment:


core_anatomic-site
   Identifier: core_anatomic-site
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: Synonymous with topography, a text string-would like to introduce a controlled
   vocabulary or ontology here.  We will use a controlled vocabulary from UMLS
   Comment:


core_organ
   Identifier: core_organ
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: Defined organ system that tissue represents
   (e.g. prostate); a text string-would like to
   introduce a controlled vocabulary or ontology here, likely UMLS.
   Comment:


core_tissue-origin
   Identifier: core_tissue-origin
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: Tissue type source, include native, transplant,
   xenograft, cell line, OTHER Specify
   Comment: Attributes are optionally available for this element
      Attribute: name is procedure and values are "biopsy" "resection" "autopsy" "necropsy"
      Attribute: name is time_from_excision and value is time, in hours,
      from excision until tissue is placed in fixativem, expressed as a decimal number
      Attribute: name is length_of_fixation and value is time, in hours, of
      fixation, expressed as a decimal number of hours.


core_data-descriptor
   Identifier: core_data-descriptor
   Version: 1.0
   Language: English (en)
   Obligation: optional
   Datatype Character String
   Maximum Occurrence: Unlimited
   Definition: A definition of the entity which the core is meant to
   represent, e.g. prostatic adenoarcarcinoma
   Comment:


core_data-descriptor_QC
   Identifier: core_data-descriptor_QC
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: Comment  specifically as Adequate or Not Adequate for quality of core to represent
   donor block diagnosis info specified for this core.
   Comment:


core_clinical-info
   Identifier: core_clinical-info
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: Relevant pre-operative information about donor, free format,
   may be pointer to a URL, should not contain any confidential information
   or identifiers.
   Comment:


core_clinical-info_id
   Identifier: core_clinical-info_id
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: URL or person to contact about tissue and clinical follow-up if available.
   Comment:


core_clinical-info_availability
   Identifier: core_clinical-info_availability
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This element has values yes or no indicating whether
   there IS or IS NOT, respectively, clinical follow-up available.
   Comment: Controlled Value


core_histo-repository
   Identifier: core_histo-repository
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This element contains a name for the institution
   providing the core_hist or a URI where this information can be
   obtained
   Comment:


core_histo-repository_specimen-id
   Identifier: core_histo-repository_specimen-id
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This element contains an identifier for the donor block
   as specified by the institution defined by the histo_core_repository.
   In most cases, this should not be the original surgical pathology
   identifier, but a minimally de-identified string (or de-linked if
   regulations have required this degree of serverance) that can be used to
   track the origins of the donor block or to relate it to other cores in
   other blocks from the same specimen.
   Comment:


core_histo-repository_specimen-diagnosis
   Identifier: core_histo-repository_specimen-diagnosis
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is the main line diagnosis for the specimen from which
   the donor block was obtained.  For example, this might be lung
   adenocarcinoma but the donor block is histopathologically normal or
   emphysema.  Specify here the primary for metastatic
   disease if known (eg. Colon adenocarcinoma metastatic to liver)
   Comment:


core_histo-repository_donor-block
   Identifier: core_histo-repository_donor-block
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is some identifier or URL that uniquely
   specifies the tissue block from which the core was taken.
   Comment:


core_histo-repository_donor-block_drill-site
   Identifier: core_histo-repository_donor-block_drill-site
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is the location in the donor block from which
   the core was taken.
   Comment: It can be provided as coordinates or as description, but
   the description of the site must be explained adequately either
   within this document or at a URI.


core_histo-repository_donor-block_drill-site_diagnosis
   Identifier: core_jostp-repository_donor-block_drill-site_diagnosis
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is the diagnosis for the specific tissue region
   for the core as drilled from the donor.  For example, this might
   be lung adenocarcinoma or histopathologically normal or emphysema.
   This is free text.  However, in the interest of facilitating searches
   of the database, we would urge users to adhere to NCI accepted
   nomenclature where defined.
   Comment:


core_results
   Identifier: core_results
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Empty
   Maximum Occurrence: Unlimited
   Definition:  Empty element that contains the other elements
   related to _core_results
   Comment:


core_results_slide-id
   Identifier: core_results_slide-id
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Empty
   Maximum Occurrence: Unlimited
   Definition: The slide identifier for the core results
   Comment:


core_results_method-of-reading-data
   Identifier: core_results_method-of-reading-data
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition:  A textual description of how the data was read, which can
   information regarding whether the data was read by an individual or
   individuals (and their names) or was read by an automated fashion.
   A description of image analysis hardware, software, manufacturer,
   version numbers, and the name of the data manager.
   Comment: Attributes are optionally available for this element
      Attribute: name is process and key is "automated" or "manual"
      Attribute: name is protocol and key is a URI


core_results_number-of-nuclei-counted
   Identifier: core_results_number-of-nuclei-counted
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Integer
   Maximum Occurrence: Unlimited
   Definition: This only for FISH, should be an integer.
   Comment:


core_results_tissue-intensity
   Identifier: core_results_tissue-intensity
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Decimal number
   Maximum Occurrence: Unlimited
   Definition: If the results of staining can be represented by an
   intensity number, the number can be included in this element.
   Comment:


core_results_percent-tissue-staining
   Identifier: core_results_percent-tissue-staining
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Decimal number ranging from 0 to 100.
   Maximum Occurrence: Unlimited
   Definition: If the results of staining can be represented
   by a percentage, then this element can be used to contain the data.
   Comment:


core_results_compartment-staining
   Identifier: core_results_compartment-staining
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: If the staining is restricted to particular organelle(s),
   they can be listed in this element.
   Comment:


core_results_staining-pattern
   Identifier: core_results_staining-pattern
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: If the staining has an identifiable pattersn, then
   this information can be included in this element.
   Comment: Some values are dot, linear, granular, patternless, diffuse


core_image
   Identifier: core_image
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Empty
   Maximum Occurrence: Unlimited
   Definition:  Empty element that contains the other elements
   related to _core_image
   Comment:


core_image_slide-id
   Identifier: core_image_slide-id
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Empty
   Maximum Occurrence: Unlimited
   Definition: The slide identifier for the core image
   Comment:


core_image_identifier
   Identifier: core_image_identifier
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: This is the URI for the image.  A URI can be a file name
   and including path.
   Comment:


core_image_format
   Identifier: core_image_format
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Character String
   Maximum Occurrence: Unlimited
   Definition: Image format
   Comment: Examples are jpeg, tiff, png.


core_image_checksum
   Identifier: core_image_checksum
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Integer
   Maximum Occurrence: Unlimited
   Definition: This is a key value pair consisting of the algorithm for
   one-way hashing (md_5, SHA, SHA256, etc.) followed by the hash number.
   Comment: Used to authenticate the image.
   Comment:


core_image_magnification
   Identifier: core_image_magnification
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Integer
   Maximum Occurrence: Unlimited
   Definition: This is the magnification at which the image was recorded.  This should be as an
   integer ranging from 1 to 1000.
   Comment:


core_image_pixel-size
   Identifier: core_image_pixel-size
   Version: 1.0
   Registration Authority: Association for Pathology Informatics
   Language: English (en)
   Obligation: Optional
   Datatype: Integer
   Maximum Occurrence: Unlimited
   Definition: This is the number of pixels used to cover the area of the image
   Comment: (or do we assume round and use diameter.)