Scientific Collections

Glossary of Terms

A common vocabulary with clear definitions promotes effective communication. As collections management throughout the USGS expands, this list of terms will grow and definitions may change. The Glossary below is the most recent version as of September 10, 2019. Please see the Updates section for more information on any revisions.

4-Point Standard—The minimum standard information needed to evaluate collections for retention are: (1) What - sample number assigned in the field or other unique identifier, as well as descriptive information pertaining to what is being collected; (2) Where - geographic information locating where the samples or specimens were collected; (3) Who - collector; and (4) When - date collected. [3]

Accessioning—The process of formally accepting and establishing permanent legal title (ownership) and/or custody for an object or specimen or group of objects and/or specimens. [16] (see also deaccession)

Acquisition—A transaction whereby one or more objects and (or) specimens is or are acquired in the same manner from one source at one time for a particular collection. Property management term equivalent to accessioning.

Active collection—Collection containing materials from ongoing research that are actively used by the project scientists. New samples are added as the research continues. Upon completion of the research topic, the materials will be evaluated for long-term retention in an appropriate repository as a resource collection. [3]

Active repository—A facility with policies and procedures that govern the long-term management of the collections in its care. Geologic repositories contain both samples and their related geoscience data. (see also ephemeral repository; inactive repository) [3]

Ancillary records—Papers (e.g., field notes, sample location maps, analytical results, photographs, etc.) that are directly related to collection items. [3] (see also associated documents; associated records)

Appraisal—The process of identifying materials offered to an archive that have sufficient value to be accessioned. [6]  The process of determining the length of time records should be retained, based on legal requirements and on their current and potential usefulness. [6]

Art and Architecture Thesaurus (AAT)—Controlled vocabulary for describing items of art, architecture, decorative arts, archival materials, and material culture. The AAT contains only generic terms, not proper names. Used by museums, art libraries, archives, catalogers, and researchers in art and art history.

Associated documents—The field notes, maps, analytical results, and other documentary evidence that accompany an object-based collection. All documentation generated by the activity of collecting and analyzing specimens or objects or other resources that are or subsequently may be accessioned, such as site forms, field notes, drawings, maps, photographs, slides, negatives, films, digital files, video and audio recordings, oral histories, laboratory reports. [1]

Associated records—Original records (or copies thereof) that are prepared, assembled and document efforts to locate, evaluate, record, study, preserve or recover a prehistoric or historic resource. Some records such as field notes, artifact inventories and oral histories may be originals that are prepared as a result of the field work, analysis and report preparation. Other records such as deeds, survey plats, historical maps and diaries may be copies of original public or archival documents that are assembled and studied as a result of historical research. Classes of associated records (and illustrative examples) that may be in a collection include, but are not limited to:

(i) Records relating to the identification, evaluation, documentation, study, preservation or recovery of a resource (such as site forms, field notes, drawings, maps, photographs, slides, negatives, films, video and audio cassette tapes, oral histories, artifact inventories, laboratory reports, computer cards and tapes, computer disks and diskettes, printouts of computerized data, manuscripts, reports, and accession, catalog and inventory records);

(ii) Records relating to the identification of a resource using remote sensing methods and equipment (such as satellite and aerial photography and imagery, side scan sonar, magnetometers, subbottom profilers, radar and fathometers);

(iii) Public records essential to understanding the resource (such as deeds, survey plats, military and census records, birth, marriage and death certificates, immigration and naturalization papers, tax forms and reports);

(iv) Archival records essential to understanding the resource (such as historical maps, drawings and photographs, manuscripts, architectural and landscape plans, correspondence, diaries, ledgers, catalogs and receipts); and

(v) Administrative records relating to the survey, excavation or other study of the resource (such as scopes of work, requests for proposals, research proposals, contracts, antiquities permits, reports, documents relating to compliance with section 106 of the National Historic Preservation Act (16 U.S.C. 470 f), and National Register of Historic Places nomination and determination of eligibility forms). [9]

Biobank—A large collection of biological or medical data and tissue samples, amassed for research purposes.

Biopreservation—The use of natural or controlled microbiota or antimicrobials as a way of extending shelf life.  Beneficial bacteria or the fermentation products produced by these bacteria are used in biopreservation to control spoilage and render pathogens inactive.

Biorepository—A biological materials repository that collects, processes, stores, and distributes biospecimens to support future scientific investigation.  Biorepositories can contain or manage specimens from animals, including humans, and many other living organisms.

Biosecurity—Procedures intended to protect humans or animals against disease or harmful biological agents.

Biospecimen—Samples of materials, such as urine, blood, tissue, cells, DNA, RNA, and protein from humans, animals, or plants. Biospecimens are stored in a biorepository and are used for laboratory research.

Biotechnology—The exploitation of biological processes for industrial and other purposes, especially the genetic manipulation of microorganisms for the production of antibiotics, hormones, etc.

Board of survey—A standing or ad hoc committee, generally appointed by senior management officials, typically consisting of three to five members serving a fixed term, and charged with the review or investigation of incidents involving loss, damage or destruction of Federal property; determination of financial liability for loss or damage of such property; and authorization for removal of items, if accountable, from official property records. Boards of Survey shall review and investigate above-cited incidents equally for accountable and non-accountable Government personal property. [10]

Buffer—Any material that attenuates fluctuations in relative humidity (RH) of the air enclosed in a volume such as a cabinet. For example, cotton dust covers can buffer against the effects of changes in RH and temperature to the objects that they cover; silica gel can buffer changes in RH within a display case caused by turning lights on and off.

Catalogverb: The act of classifying objects into categories and documenting them with descriptive detail and identifying or descriptive unique numbers. noun: A file or database composed of systematically arranged records. A catalog of scientific collections is the primary tool for organizing and sharing information about collections and accessible through a digital environment at a USGS office or Science Center. [16]

Catalog record—A standardized record that contains detailed information about an object, specimen, or lot in a collection. [1]

Chain of custody—The documentation of sample ownership by successive parties; the principle of documenting where a sample originated, where it is currently located, and all intermediary steps that have occurred from acquisition through accession. This documentation begins with the collecting scientist, accompanies the sample throughout its research history, and is incorporated into the repository’s permanent records. [3]

Collection—A long-term research asset, as opposed to an expendable research supply. A collection can be considered to be a set of specimens that are catalogued together in one database or numbering system. [5] Deliberate grouping of objects assembled according to a rational scheme. The many types of collections that are defined in this glossary include: scientific collections, working collections, institutional collections, museum property collections. Material that is excavated or removed during a survey, excavation or other study of a biotic, marine, terrestrial, prehistoric or historic resource, including their associated records that are prepared or assembled in connection with the survey, excavation or other study. [9]

The Geologic Collections Management System (GCMS) added the following categories of collections in 2011. The first set of categories relate to the purpose of the collection being defined: reference collection (which contains samples of a distinct nature that provide an objective standard against which other samples are compared [a reference collection may be augmented with new samples as knowledge of the material grows; and collections of “type” fossils or rocks are examples of reference collections]), field collection (considered the fundamental “suite of closely related samples for a unified study purpose”), sample collection (which results when a single sample is broken into its component parts for study), research collection (which pulls together various field collections and is defined by disciplinary, temporal, or geographic parameters), directed research collection (which is a specifically targeted subset of a research collection such as a group of samples from disparate field collections that are used for a single research study), and at the highest level in the GCMS, a general collection (which gathers research collections that exhibit similarities of sample type or geography). [3]

GCMS suggest a second set of categories that are based on their status. Active collections (also known as working collections) contain materials from ongoing research that are actively used by the project scientists with new samples being added as the research continues. Upon completion of the research topic, the materials will be evaluated for permanent retention in a GCMS repository as a resource collection. Resource collections contain materials, from completed research projects or topics, which remain significant as research assets and are made available for current and future research. Resource collections form the bulk of GCMS materials and are expected to be preserved for an indefinite period of time. Legacy collections stored by the USGS contain samples that were collected by research scientists who are no longer with the Survey. If sufficient documentation is available, these collections will be incorporated in the GCMS and become resource collections.  ‘Active,’ ‘resource,’ and ‘legacy’ collections refer to samples already in USGS custody. Collections that will be created and added to the GCMS in the future under the policies and procedures set out in the GCMS policy documents as new collections. Orphan collections are those that, for a variety of reasons, such as the lack of pertinent sample data, are deemed to have little foreseeable research value and will not be included in the GCMS. [3]

Collections management—The ongoing process of acquiring and maintaining collections. It defines the policies and procedures that govern sample handling, labeling, storage, cataloging, conservation, and access to the samples. [3]

Collection Plan—A document established during the Project Work Plan process for new USGS research and approved by the Science Center Director that documents, at a high level, the planning for, management and expected disposition of the working collection. The Collection Plan is a living document and may be amended over the lifespan of the collection. Key requirements for a Collection Plan are provided in the Guide to Planning for and Managing Scientific Working Collections in the U.S. Geological Survey. [16]

Collections policy—The document that guides the content of the collections to be compatible with the USGS mission of earth sciences research and guides collection decisions to be prudent, responsible, and informed. By providing the basis for procedural actions, the policy presents a consistent context for decisions regarding the handling, retention, and disposition of samples and ensures that collections are managed according to specific standards and strategies.

Collecting units—Those projects and personnel authorized by the Director of the Geological Survey to conduct field studies and collect physical samples in the course of their research. [3]

Consumptive use—The act or process of using a specimen or object, or a portion thereof, in a way that causes damage or deterioration to it. Destructive analysis is a legitimate example of consumptive use for approved scientific research purposes.

Content type—This is a categorical variable that describes the different types of samples and specimens associated with each collection record within an institution.  Multiple values will be allowed in each collection record. [5]

Conveyance of museum objects—In accordance with title 54, "[t]he secretary may convey museum objects that the Secretary determines are no longer needed for museum purposes, without monetary consideration but subject to such terms and conditions as the Secretary considers necessary, to private institutions exempt from Federal taxation under section 501 (c)(3) of the Internal Revenue Code of 1986 (26 U.S.C. 501 (c)(3)) and to non-federal governmental entities if the Secretary determines that the recipient is dedicated to the preservation and interpretation of natural or cultural heritage and is qualified to manage the property, prior to any conveyance under this subsection and subsection (g.)" [13]

Critical redundancy—Research organizations keep collections in different places and maintain large collections of similar specimens for several reasons such as in the event of natural disaster. [5]

Cryopreservation—A process where cells, whole tissues, or any other substances susceptible to damage caused by chemical reactivity or time are preserved by cooling to sub-zero temperatures.

Curator—Person responsible for collection management. [3]

Data—Facts, figures, or other items of information organized for and by analysis. [3]

Daughter sample—A sample that constitutes a subset of the original sample. [3]

Deaccession—The process by which a specimen or collection is formally and permanently removed from custody. Examples of deaccessions are exchanges, transfers, and losses. [1] (see also accession) Note: This is not to be confused with weeding, which is the process of identifying and removing items from a larger body of materials. [6]

Desiccant—A drying agent that withdraws water from other materials. An example of a soluble desiccant is glycerol; an example of an insoluble desiccant is silica gel. [15]

Destruction of museum objects—In accordance with Title 54, "[t]he Secretary may destroy or cause to be destroyed museum objects that the Secretary determines to have no scientific, cultural, historic, educational, esthetic, or monetary value." [13]

Directed research collection—A specifically targeted variety of research collection, such as a group of samples from several different field collections that are used for a single research study. (see research collection) [3]

Discovery—Identifying the existence and whereabouts of desired data and collections in addition to determining their availability, quality, and format. Discovery can occur in a variety of ways: the Internet provides one means of access to computerized records, whereas attribution at the end of journal articles, for example, leads the reader to a source of information. [8]

Disposition—The outcome of the collection evaluation process that determines that a collection, or portion thereof, is to be retained, transferred or destroyed in accordance with applicable Bureau requirements. [16]

Ephemeral repository—A temporary storage arrangement with no provision for identifying, recording, or preserving the specimens contained therein. (see active repository) [3]

Exchanges—In accordance with Title 54, “[t]he Secretary [of the Interior] may make exchanges by accepting museum objects and other personal property and by granting in exchange for the museum objects or other personal property museum property under the administrative jurisdiction of the Secretary that no longer is needed or that may be held in duplicate among the museum properties administered by the Secretary. Exchanges shall be consummated on a basis that the Secretary considers to be equitable and in the public interest.” [13] (see also deaccession; transfer)

Field collection—A collection gathered during the course of a researcher’s field work and considered the fundamental instance of “a set of specimens that have been brought together on the basis of some common characteristic.” (see also sample collection) [3]

Fossil—The remains or traces of living things from the geologic past preserved in rock, sediment, or other substrate (e.g., ice, tar, amber, etc.). [3] Fossils collections conventionally are categorized by the type of organism (vertebrate, invertebrate, etc.)

Fundamental Science Practices (FSP)—The set of mandated requirements, codified in USGS policy, that describe the peer review process for publishing research results, releasing data, and other aspects of the scientific process conducted by USGS scientists. [17]

GenBank—The NIH genetic sequence database, an annotated collection of all publically available DNA sequences.

General collection—A high-level collection that gathers research collections that exhibit similarities of sample type or geography, for example all USGS fossils collected within the United States. (see also collection) [3]

Geologic Collections Management System (GCMS)—A management plan and outline catalog for the coordination of USGS collections of geological samples from various locations within the United States, published as USGS Circular 1410. [3]

Holotype—1. A single physical specimen designated by an author as the type of a species or lesser taxon at the time of establishing the group. 2. The type of a species or lesser taxon designated at a date later than that of establishing a group or by a person other than the author of the taxon. [7]  The single specimen designated as the type of a species by the original author at the time the species name and description was published. [12]

Iconic value—Having important or special worth, be it for historical or institutional reasons (e.g., a former Director’s field collections or collections from the founding surveys of the USGS). [3]

Inactive repository—A sample storage facility that does not actively manage the collections stored there. (see also active repository; ephemeral repository) [3]

Informatics—The use of computer science hardware and software to manage, compile, analyze, interpret, and display data. [5]

Infrastructure—The basic physical and organizational structures and facilities needed for the operation of a society of enterprise.

Interagency Working Group on Scientific Collections (IWGSC)—A Federal committee that was convened to develop common strategies for the management of scientific collections. This group included representatives from Federal agencies with scientific collections (Smithsonian Institution, BLM, NASA, NOAA, NPS, USFS, USGS). [3]

International Geo Sample Number (IGSN)—Unique international sample identifier number administered by the System for Earth Sample Registration (SESAR). [3]

Integrated Taxonomic Information System (ITIS) (http://itis.gov)—Database of reliable information on biological species names and their hierarchical classification that includes documented taxonomic information of flora and fauna from both aquatic and terrestrial habitats. The database is peer-reviewed periodically to ensure high quality with valid classifications, revisions, and additions of newly described species. (see also Taxonomic Serial Number [TSN])

Institutional collections—see Scientific Collection.

Institutional discipline—This is a categorical variable associated with each institutional record.  Multiple values are allowed in each record to accommodate institutions like natural history museums which may cover biology, anthropology and mineralogy, for example. [5]

Inventory—An itemized listing of objects; the act of physically locating all or a random sample of the items of a collection for which a unit is responsible. Physical inventory verifies the presence and condition of specific objects in a collection. [1]

Legacy collections—Existing collections from past research that may or may not have complete descriptions of their content, provenance, and management. These collections have not yet undergone the Collections Evaluation process. [17]

Location—The geographic site, defined in XY and sometimes Z coordinates, where the sample was originally collected. [3]

Map; to Map; Mapping—[popular vernacular] visualizing, organizing or systematizing information, and (or) relating bits of information.

Material remains—objects, specimens and other physical evidence that are excavated or removed in connection with efforts to locate, evaluate, document, study, preserve or recover a prehistoric or historic resource. [9]

Metadata—Documentation about a sample or collection that describes pertinent background information, including field information (original geographic location, collector, date, specimen number), the nature of the material, and any associated descriptive characteristics.

Museum object—“An object that typically is movable and is eligible to be, or is made part of, a museum, library, or archive collection through a formal procedure, such as accessioning. The term ‘museum object’ includes a prehistoric or historic artifact, work of art, book, document, photograph, or natural history specimen.” [13]

Museum property—An object that is collected according to some rational scheme, such as a Scope of Collections Statement, and that is formally accessioned as museum property. Museum objects may include prehistoric and historic objects, artifacts, works of art, associated documents, and natural history specimens. Elements, fragments, and components of structures may be accessed as museum property, if they are no longer a part of an original structure. Museum property does not include those items necessary to display a collection such as exhibit cases, dioramas, special lighting, graphics, replicas, etc. [1]

Museum collections—Assemblages of officially accessioned museum property collected according to some rational scheme such as a Scope of Collection Statement [1].  A collection can comprise one or more specimens or samples that have been accessioned as museum property by the USGS.

National Digital Catalog (NDC)—The National Digital Catalog includes metadata records describing geological and geophysical samples and data managed by state geological agencies and federal organizations.  The Catalog is currently being revised to allow entry of metadata records from all types of samples from new and existing USGS working collections. [17]

National Geological and Geophysical Data Preservation Program (NGGDPP)—A program created by the Energy Policy Act of 2005 to develop a national network of cooperating State and Federal repositories of geoscience materials and data that are operated independently yet guided by common standards, procedures, and protocols for metadata. The holdings of all collections will be widely accessible through a common and mirrored Internet-based catalog, the National Digital Catalog. The holdings of the individual repositories will complement each other to preserve the geoscience assets of the Nation and serve as a comprehensive source of geoscience data and materials to serve national needs today and in the future. [3]

New collection—A suite of samples that will be collected and maintained using the GCMS business plan template and made available through the GCMS interface. [3]

Nomenclature 3.0—Structured and controlled lexicon for classifying man-made object names, arranged hierarchically within functionally defined categories. De facto standard used within the community of history museums in North America for indexing and cataloging collections.

Organic act—The legislation that authorizes the establishment of any Federal agency. [3]

Orphan collection—A collection that, for a variety of reasons (such as pertinent sample data) is deemed to have little foreseeable research value, is bereft of purpose,  and/or is supported by a collector who has died or otherwise abandoned it.

Permanent collections—See institutional collection.

Personal property—Government-owned property of any kind or an interest therein, except (1) real property (land, buildings, and appurtenances), and (2) records of the Federal Government. Specifically, personal property includes all equipment, materials and supplies, and museum items which include antiques, artifacts, natural history specimens, and other items of museum collections. It does not include property which is incorporated in, or permanently affixed to, real property. Government personal property should not be confused with privately owned items. [10]

Personal property management—A process and system for controlling the acquisition, receipt, storage, issue, utilization, maintenance, protection, accountability, and disposal of personal property to best satisfy the program needs of the USGS. [10]

Preanalytic—any procedure that takes places before an analysis.

Preservation Type—This is a categorical variable that describes the different forms of preservation used by each collection record within an institution. Multiple values will be allowed in each collection record.

Procedure—A set of established forms or methods for carrying out policy. [3]

Project collection—Materials assembled specifically for short-term use and not intended for long-term preservation. [4] (see also working collection; collection)

Project Work Plan—A document that defines an approved study, setting the timeline for the research, the discrete tasks that need to be completed to accomplish the study objectives and the relationship of these tasks to one another including the methods to be used. The Project Work Plan includes the Collection Plan and is approved by the Science Center Director (also refer to SM 502.2). [16]

Proprietary period for release of data—The length of time before data should be released to the public domain. [3]

Provenance—1. The history of ownership of data or samples. [3]  2. The origin or source of something. [6]  3. Information regarding the origins, custody, and ownership of an item or collection. [6]

Record—Documentation of the business activities of a unit. Records differ from collections insofar as their inherent characteristics (typically paper or electronic files) and their purposes (records are abstract representations of activities where objects of a collection possess the intrinsic properties being studied).

In 44 USC 3301, the National Archives and Records Administration (NARA), defines official records as follows: “...’Records’ includes all books, papers, maps, photographs, machine readable materials, or other documentary materials, regardless of physical form or characteristics, made or received by an agency of the United States Government under Federal law or in connection with the transaction of public business and preserved or appropriate for preservation by that agency or its legitimate successor as evidence of the organization, functions, policies, decisions, procedures, operations or other activities of the Government or because of the informational value of data in them. Library and museum material made or acquired and preserved solely for reference or exhibition purposes, extra copies of documents preserved only for convenience of reference, and stocks of publications and of processed documents are not included.” [1]

Records management—The systematic and administrative control of records throughout their life cycle to ensure efficiency and economy in their creation, use, handling, control, maintenance, and disposition. Retention schedule: (also disposal schedule, records schedule, records retention schedule, transfer schedule), n. ~ A document that identifies and describes an organization's records, usually at the series level, provides instructions for the disposition of records throughout their life cycle. [6]

Reference collection—Different from research collections, a reference collection contains samples of a distinct nature that provide an objective standard against which other samples are compared; the reference collection may be augmented with new samples as knowledge of the material grows. Collections of type specimens are examples of reference collections. [3]

Repository—A controlled space where physical samples or specimens are safely stored, discoverable, and accessible. [16]

Re-sampling (also known as secondary sampling)—Retrieving an archived sample for the purpose of additional scientific inquiry, whether geochemical analysis, age determination, or testing of physical properties. [3]

Research collection—A subset of a general collection defined by disciplinary, temporal, or geographic parameters. (see also directed research collection) [3]

Resource collection—A suite of samples from a completed project or research topic that remains significant as research assets. They are housed in an appropriate repository and are made available for current and future research. [3]

Sample/Specimen—The terms “sample” and “specimen” are used interchangeably to refer to a unit of a collection that constitutes research materials such as a rock, an organism, or a portion thereof. [16]

Sample collection—A collection of materials broken from a single sample into its component parts for study, e.g., multiple microfossils recovered from a single sample. [3]

Sample data—Information that describes and defines a sample. [3]

Sample ID—Alpha-numeric code assigned to an individual sample to differentiate it from other samples in its collection group. Different IDs may accrue to the same sample due to processing by various analytical labs. [3]

ScienceBase—As the agency-wide framework for the comprehensive management of digital information, ScienceBase organizes and connects the various catalogs and databases within the USGS and greater geoscience community. [3]

ScienceBase catalog—The information portal providing access to the various geoscience materials, data, and information within the ScienceBase framework. [3]

Scientific collections—“Sets of physical specimens, living or inanimate, created for the purpose of supporting science and serving as a long-term research asset, rather than for their market value as collectibles or their historical, artistic, or cultural significance, and, as appropriate and feasible, the associated specimen data and materials”. Specimens in a Federal research laboratory or on Federal property are not necessarily, or automatically, part of a collection. [17]

Working Collections. “Organic or inorganic specimens and items maintained by bureau/office programs that are not intended for long-term preservation and care as museum property due to their expendable nature. Working collections are intended for use during education or ongoing research and may be consumed or discarded during the analysis process according to bureau policy. Some specimens and items may subsequently be designated museum property. Working collections will be discarded when it is determined there is no longer a need for the collection for future research or education or upon completion of the ongoing research according to standards set in bureau/office policy” (411 DM 1, 1.5 BB). [16]

Museum Collections. Assemblages of materials accessioned (officially titled) into custody at a museum or entity whose mission involves the permanent preservation of objects and/or specimens, acquired according to some rational scheme such as a Scope of Collection Statement. [15]

Secondary sampling—Re-sampling of archived material for additional scientific research. (see re-sampling) [3]

Site ID—Identifier of a specific sampling site in XYZ coordinates (i.e., sample site, core hole site, measured sections site). [3]

Software as a Service (SaaS)—Sometimes referred to as "on-demand software," is a software delivery model in which software and associated data are centrally hosted on the cloud.  SaaS is typically accessed by users via a web browser. One of the biggest selling points is the potential to reduce IT support costs by outsourcing hardware and software maintenance and support to the SaaS provider.  SalesForce and Concur Technologies are two leading SaaS companies.

The term "software as a service" is considered part of the nomenclature of cloud computing, along with platform as a service (PaaS).  With this model, a single version of the application, with a single configuration (hardware, network, operating system), is used for all customers.  This is contrasted with traditional software, where multiple physical copies of the software — each potentially of a different version, with a potentially different configuration, and often customized — are installed across various customer sites.

Configuration and customization

SaaS applications support what is traditionally known as application customization.  In other words, like traditional enterprise software, a single customer can alter the set of configuration options that affect its functionality and look-and-feel.  Each customer may have its own settings for the configuration options. The application can be customized to the degree it was designed for based on a set of predefined configuration options.  The customer cannot, however, change the page layout unless such an option was designed for.

Accelerated feature delivery

SaaS applications are often updated more frequently than traditional software, in many cases on a weekly or monthly basis.  This is enabled by several factors:

> The application is hosted centrally, so an update is decided and executed by the provider, not by customers

> The application only has a single configuration, making development testing faster.

> The application vendor has access to all customer data, expediting design and regression testing.

> The solution provider has access to user behavior within the application (usually via web analytics), making it easier to identify areas worthy of improvement.

Criticism

One notable criticism of SaaS is Service as a Software Substitute (SaaSS).  In using SaaSS, the users do not have a copy of the executable file: it is on the server, where the users can't see or touch it.  Thus it is impossible for them to ascertain what it really does, and impossible to change it. SaaS inherently gives the server operator the power to change the software in use, or the users' data being operated on.  SaaSS is equivalent to running proprietary software with a universal back door.

Standards—Specimens that are designated as permanent references that must be retained for validation and calibration. [5]

Stewardship—The responsibility to manage and preserve property in accordance with the policies and procedures of the sponsoring agency or institution.

Subsample—See daughter sample.

System of Earth Sample Registration (SESAR)—A centralized registry that provides and administers unique identifiers for geoscience samples--the International GeoSample Number (IGSN). SESAR is supported by the National Science Foundation and managed as part of the Geoinformatics for Geochemistry Program.

Systematic biology, systematics—A research field within biology that deals with the evolution and taxonomy of organisms. [5]

Taxonomy, taxonomic—Taxonomy is a research field within biology that deals with the classification and naming of organ­isms. A taxon is a single category of organisms. [5]

Taxon (pl. taxa)—A taxonomic category or group, such as phylum, class, order, family, genus, or species.

Taxonomic Serial Number (TSN) (http:www.itis.gov/pdf/faq_itis_tsn.pdf)—Unique, persistent, non-intelligent identifier for a scientific name in the context of the Integrated Taxonomic Information System (ITIS).  A TSN is the primary key for the IT IS scientific name table.

Transfer of museum objects—In accordance with Title 54, “[t]he Secretary may transfer museum objects that the Secretary determines are no longer needed for museum purposes to qualified Federal agencies, including the Smithsonian Institution, that have programs to preserve and interpret cultural or natural heritage, and accept the transfer of museum objects directly to the administrative jurisdiction of the Secretary for the purpose of this chapter.” [13]

Type specimen—The specimen, or each of a set of specimens, on which the description and name of a new species, mineral phase, or rock type is based. For taxonomists, the most critical kind of voucher specimen. [5][14]

There are several categories of types; the most common are as follows: [12]

The following list combines similar definitions by the International Code of Zoological Nomenclature and the International Plant Science Center, New York Botanical Garden: Holotypes, syntypes, lectotypes, and neotypes are the bearers of the scientific names of all nominal species-group taxa.

Holotype: The single specimen upon which a new nominal species-group taxon is based in the original publication and designated as the type of a species by the original author at the time the species name and description was published.

Isotype: A duplicate specimen of the holotype.

Syntype: Any one of the multiple specimens on which a species-group name is equally based when no holotype was specified in the original publication and no subsequent designation of a lectotype has been published.  Any of two or more specimens listed in the original description of a taxon when a holotype was not designated.

Isosyntype: A duplicate of a syntype.

Paratype: A specimen not formally designated as a type but cited along with the type collection in the original description of a taxon.

Lectotype: One specimen selected from two or more syntypes upon which a species-group name is originally based and designated in a publication subsequent to the original description to become the unique name bearer. A specimen chosen by a later researcher to serve as if it were the holotype. It is chosen from among the specimens available to the original publishing author (isotypes, syntypes, and/or paratypes) of a scientific name when the holotype was either lost or destroyed, or when no holotype was designated.

Neotype: A specimen chosen as the name bearer of a species-group taxon if no holotype, lectotype, syntype, or prior neotype is believed to be extant. A specimen chosen by a later researcher to serve in place of a holotype when all specimens available to the original publishing author of a scientific name have been lost or destroyed.

Topotype: A specimen of a plant collected from the same locality as the holotype and usually on a different date. A topotype has no formal standing. Also referred to as a “locotype.”

Cotype: A term formerly used for syntype and sometimes [erroneously] for isotype and paratype. This is an old term that was used loosely and is not used by today’s taxonomists.

Generitype: The type specimen of a genus. It is designated by using the type for the name of a particular species within that genus. For example, the generitype for Aster is the type for Aster amellus L.

Universally Unique Identifier (UUID)—A designation assigned to each sample to distinguish it from all other samples in the GCMS. Use of a UUID prevents ambiguity by systematizing sample designation and ensures that all information associated with a sample is preserved for accessibility on a global scale. [3]

Voucher specimen—A specimen that physically and permanently documents data in published literature by verifying the identity of the organism(s) used in the study and by doing so ensures that a study which otherwise could not be repeated can be accurately reviewed or reassessed. For example, rock and mineral specimens may serve as vouchers to document the geology of an area. [17]

Weeding—The process of identifying and removing unwanted materials from a larger body of materials. [6]

Working collections—see Scientific Collection.

 

References

[1] Department of the Interior Manual, Part 411 (“411 DM”), Identifying and Managing Museum Property: http://elips.doi.gov/ELIPS/DocView.aspx? d=3519http://elips.doi.gov/ELIPS/DocView.aspx?id=3519

[2] U.S. Geological Survey Manual (“Survey Manual” and “SM”): https://www2.usgs.gov/usgs-manual/

[3] The Geologic Materials Repository Working Group, 2015, The USGS Geologic Collections Management System (GCMS): A Master Catalog and Collections Management Plan for USGS Geologic Samples and Sample Collections: http://dx.doi.org/10.3133/cir1410

[4] John Holdren, Director, Office of Science and Technology Policy (OSTP) Memorandum dated March 20, 2014: https://www.whitehouse.gov/sites/default/files/microsites/ostp/ostp_memo_scientific_collections_march_2014.pdf

[5] Interagency Working Group on Scientific Collections (IWGSC), 2009, Scientific Collections: Mission-Critical Infrastructure for Federal Science Agencies: https://www.whitehouse.gov/sites/default/files/sci-collections-report-2009-rev2.pdf

[6] Society of American Archivists, 2005, A Glossary of Archival and Records Terminology by Richard Pearce Moses: http://www2.archivists.org/glossary

[7] Webster’s New Collegiate Dictionary

[8] National Research Council of the National Academies, 2002, Geoscience Data and Collections: National Resources in Peril: http://www.nap.edu/catalog.php?record_id=10348

[9] 36 CFR 79 <https://www.law.cornell.edu/cfr/text/36/79.4>

[10] USGS Property Management Handbook: http://www.usgs.gov/usgs-manual/handbook/hb/408-2-h.html#c1

[11] 44 USC 3301: http://uscode.house.gov/view.xhtml?req=granuleid:USC-prelim-title44-section3301&num=0&edition=prelim

[12] International Plant Science Center, The C.V. Starr Virtual Herbarium,  The New York Botanical Garden,http://sciweb.nybg.org/science2/herbarium_imaging/typedefinition.asp.html

[13] 54 USC Section 102502: https://www.congress.gov/bill/113th-congress/house-bill/1068/text?overview=closed

[14] Oxford Dictionaries Online: http://www.oxforddictionaries.com/us/definition/american_english/type-specimen

[15] DOI Museum Property Directive 4: https://www.doi.gov/sites/doi.gov/files/migrated/museum/policy/upload/Dir-4_Required-Stds-Collections-Preservation.pdf

[16] USGS Survey Manual Instructional Memorandum (IM) IM CSS 2019-01: USGS Policy on Scientific Working Collections: https://www.usgs.gov/about/organization/science-support/survey-manual/im-css-2019-01

[17] USGS Guide to Planning for and Managing Scientific Working Collections in the U.S. Geological Survey: https://www.usgs.gov/products/scientific-collections/guide-planning-and-managing-scientific-working-collections-us

 

Updates

June 28, 2017: The original Collections Glossary of Terms is uploaded.

January 12, 2018: Definitions have been updated for selected terms to make them consistent with ongoing USGS CSC work to develop scientific collections policy.

March 6, 2018: Definitions for institutional, working, and museum collections have been updated, and included underneath the general definition for scientific collections.

September 10, 2019: Definitions have been updated to match those provided in IM CSS 2019-01, USGS Scientific Working Collections Management and the Guide to Planning for and Managing Scientific Working Collections in the U.S. Geological Survey