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.)