Quick id

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Contributing authors: Frank Gibson, Dirk Derom

This document is in flux and will evolve we are not soliciting feedback as yet. However, if you want to comment on a document that may change rapidly please use the Discussion option for this page

Status: Document in progress About this document

This document gives both the rationale and instructions on how to add quick terms to the OBI. A step by step guide should allow anyone to add terms to the OBI, and limited knowledge about the OBI is required. Nevertheless it is strongly recommended to get familiar with ontology design before adding terms to the OBI.

How to use this document?

This page is created both to explain the actual procedure of adding terms to OBI, as it is a description of the idea behind the Quick ID procedure. It is subdivided into different sections, so one can choose to

  • Simply learn how to add terms
    The section 'Submit a term to OBI ' describes the procedure on adding terms to OBI. Useful for those who are familiar with OBI and need a simple tutorial on how to add terms.
  • Get familiar with the Quick ID procedure
    All other sections are created to help you understand the procedure. This includes:
    • Introduction to the QUICK ID
      A short introduction to Quick ID to get you going.
    • Glossary of common terminology
      This glossary will explain frequently used terms, which hopefully helps to understand this procedure. This glossary is a guide explaining these terms, and refers to those documents with detailed explanation of the particular concept.
    • Mailinglistfor Quick ID's
      If you have further questions, you can always contact us using [the Quick ID mailinglist].
      (read this document on how to use a mailinglist).



Introduction to the Quick ID?

This section is both an introduction to the Quick ID procedure. Read through this section if you are not (really) familiar with the Quick ID procedure.

Quick ID's refers to a procedure developed to quickly add terms to the OBI (ID's in "Quick ID's" refer to ID's given to the terms when added to the OBI repository). Quick ID's therefore refers to the process of quickly adding terms to the OBI, without the necessity of being a core developer of OBI. The Quick ID process is a process to allow those individuals who might not be strongly involved in the design of OBI, to add terms to the OBI repository.

Quick Id's are created for those who want to contribute/support to the OBI targeting those individuals who are not directly involved or familiar with ontology design. Adding terms through the procedure of Quick ID, allows for fast additions with a minimal learning curve. It's procedure is despite it (relatively) simplicity, nevertheless very powerful. It's combination of curation and openness enables a fast growing ontology created by and for the community.

The benefits of the Quick ID procedure for OBI are:

  • Direct input from the scientific community
  • Input from various fields using a single procedure
  • Curate the OBI and maintain influx from the community
  • Reduced load on curation through expert input

Contributors through the Quick ID benefit from:

  • Small load on contribution
  • Hands on control of the OBI and their domain specific ontology (terminology)
  • More robust ontology integration by shared expertise
  • Improved speed for the construction and extension of OBI and the domain specific ontology

Quick Terms hold a special position within OBI. It is fully part of the OBI, however needs to be curated before being submitted to the OBI. This curation process normally has a small load, and enables the development of a well-structured OBI. Initially, a Quick Term has the status of uncurated. This means that these terms are not (yet) part of what you could call the core OBI. A developer of OBI then checks the submitted term and adds it to the OBI. Normally, when the Quick Term is added according the following instructions, this process is semi-automatic. For a Quick Term to be added quickly to the OBI, it is therefore important to follow the instructions.

Quick ID is created for all who want to add terms to the OBI. The goal of OBI is to create an integrated ontology for the description of life-science and clinical investigations. Anyone involved in the life-sciences or clinical investigations is welcomed to contribute to OBI. The power of OBI is driven by the input of these various fields. The Quick ID process is an expression of this emphasis on open access and development.
Any questions regarding the Quick ID's can be asked [here ?mailinglist for Quick ID?].



BFO, OBI and Quick ID

In short

Quick ID's is a file within OBI, and OBI uses BFO as an upper ontology. The Quick ID file allows to add terms into OBI, but needs to be curated before being added to the 'core' OBI repository.


BFO

The following information is gathered from BFO and is a (very short) summary which hopefully allows to grasp the basics of the BFO. For a full description of Basic Formal ontology (BFO), go to the BFO website.

An ontology tries to represent the reality creating a controlled value list (different terms) to describe ('represent') the reality of the domain. A scientific ontology tries to represent the reality investigated by the sciences. But representing such a reality must be valid across various domains in order to exchange our data easily. Constructing specific ontologies only applicable to a specific domain is not very useful since it still does not allow to integrate the data from those fields. BFO is a framework that allows those various domains to be connected using the BFO framework.

Therefore the BFO is a top-level (or upper or formal) ontology. It's main characteristics are:

  • top-level
    As mentioned before it is the overall framework designed to integrate domain ontologies.
  • Holds categories containing or representing universals primarily
    The goal of BFO is not to develop ontologies as such, but to organize domain ontologies (e.g. an ontology for the neurosciences, the genetic ontology...). Universals are the 'abstract' or 'general' structure (e.g. "human", "mammal" or "feline"). These universals are the focus of BFO.
  • Uses perspectivalism
    Many different representations that are equally good (good in the sense of being true) precisely in that they capture different and important features of one and the same reality (different 'perspectives' enhance our understanding of the studied subject).
  • It's extended downward
    When the BFO will be extended (cf. 'capture' more and more domains and thus studied subjects) this will be done through its domain ontologies. It is believed that the BFO holds the classes needed for the construction and development of detailed domain ontologies. As such, this framework is thought to be stable and extensive.

To sum it up: BFO is a top-level (dealing with only universals, say working on an 'abstract level') ontology (cf. the attempt to describe or represent reality) which allows domain specific ontologies (such as OBI) to describe reality by differentiating between the characteristics (e.g. 'is this a process or not') of the particular element (e.g. 'a heart') one wants to describe.


OBI

The Ontology for Biomedical Investigations project (cf. OBI) is developing an integrated ontology for the description of biological and clinical investigations (and therefore is a domain specific ontology in contrast with the top-level ontology BFO). This includes a set of 'universal' terms, that are applicable across various biological and technological domains (originating from BFO), and domain-specific terms relevant only to a given domain (OBI specific terms). This ontology will support the consistent annotation of biomedical investigations, regardless of the particular field of study. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. In other words: OBI uses the 'framework' of BFO and builds an ontology within this framework which allows to connect data from different fields.


Quick Terms

The Quick ID file (cf. obi-quick-id.owl) is a specific file within OBI, which (since being part of the OBI) also uses the BFO. It's a protocol developed for those who have values they think are part of the OBI domain specific ontology, but are not core developers of OBI as such. This protocol allows those individuals to add terms in an easy manner.

The Quick ID procedure is built around the obi-quick-id.owl file. It's basically a file within the OBI ontology which holds all newly added terms. Adding a term through the Quick ID adds those terms to the Quick ID file (within OBI). This file is different from other OBI files, due to the fact that all terms initially are 'uncurated'. Though it's part of the OBI, the terms added through Quick ID are not immediately part of the core OBI, but need curation before added to the core OBI. When terms are added correctly this is a semi-automatic process.

Additional Information

When you start out with OBI, it is not surprising that the specific terminology is confusing. Therefore we provide a short glossary of terms used in BFO, OBI and Quick ID. It's gives both a short description as (if applicable) where to find additional information.

If this document nevertheless does not answer all your questions, you can join our mailinglist for Quick ID.

The process for quickly allocating OBI ids for accepted simple cross product terms can be found here along with some examples.

Submit a term to OBI

Before you start...

When you want to add terms through the Quick ID procedure, it is assumed that you:


Set obi-quick-id.owl as the active ontology file

Once selected as active all new classes added to the ontology via Protege will be added to the obi-quick-id.owl file. You can set the obi-quick-id.owl file as the active ontology file following the instructions outlined in section II of the use Protege with OBI document.

When set as active, the file 'obi-quick-id.owl' (and only obi-quic-id.owl) should no longer be in italic and have a different background color than the other files.

obi-quick-id.owl set as active

Determine the node of the Basic Formal Ontology

The following instructions will help you determine where under BFO your term should go and therefore how to describe and annotate it for inclusion within OBI. When submitting a term to OBI consideration should be given as to which node of BFO the term should be inferred under. This section allows you to determine whether the term you would like to add is a

  • process
  • material entity
  • information that describes an entity

Using the definition of process, material entity or information that describes an entitiy (which are all BFO classes), one can determine under which class the particular term should go to. Each term should fit in one of these classes. Therefore, you should start with process and move on untill you found the class appropriate for your Quick Term. It is always a good idea to read through all the classes, even if you 'are sure' which class it should go under.

Use the following table to determine the class. In the first column you find the actual BFO class and in the second the definition and explanation of the particlar class. Examples are used to further assist you in determining the class. Once you decided which class corresponds to your term, click on the class which brings you to the next step.

BFO Class Explanation

process

Definition
A "span:ProcessualEntity" ("processual_entity") that is a maximally connected spatio-temporal whole and has bona fide beginnings and endings corresponding to real discontinuities.

Example: process of sleeping

  • span:ProcessualEntity and processual_entity
    Both span:ProcessualEntity and processual_entity come from the terminology used in BFO. In this stage it is not important to know where they are referring to, but you can always check the [glossary] for more information.
  • maximally connected spatio-temporal whole
    A process has both spatial and temporal 'parts'. Both spatial and temporal parts are tightly connected and therefore defined as 'maximally connected spatia-temporal whole. One example is the John's life can be described as 'when he was a child', 'when he was an adult'... (= temporal part) and they are tightly connected with the spatial parts as in 'when he lived in Seatle', 'when he lived in New York'...
    In the case of sleeping: sleeping is clearly stretched over time (e.g. from 9am till 1pm) and is tightly connected with the place one was sleeping (in bed, on the couch, in a haystack...).
  • bona fide beginnings and endings
    The process must have a "real" beginning and ending, a very distinct begin point and end point.
    In the case of sleeping: beginning point = when one begins to sleep, ending point: when one wakes up
  • corresponding to real discontinuities
    The phase before the beginning point must be clearly distinguishable from the phase after the beginning point: here = being awake vs. being asleep
    The phase before ending point must be clearly distinguishable from the phase after the ending point: here = being asleep vs. being awake'.

Other examples

  • the life of an organism
  • the process of sleeping
  • the process of cell-division
  • the functioning of a heart>/li>

material entity

Material is any of

  • bfo:Object
  • bfo:ObjectAggregate
  • bfo:FiatObjectPart.
bfo:object

Definition
A bfo:object is a "snap:IndependentContinuant" ("independent_continuant") that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial "snap:Object" ("object") entities is independent of that of other entities and can be maintained through time.


Example: a heart

  • snap:IndependentContinuant and independent_continuant
    Both snap:IndependentContinuant and independent_continuant come from the terminology used in BFO. In this stage it is not important to know where they are referring to, but you can always check the [glossary] for more information.
  • spatially extended
    Refers to the fact that they take in a certain part of the space, that they have a certain spatial dimension. In the case of a heart, this means that the heart has a particular size.
  • possesses an internal unity
    The entities in this class have an 'internal unity' as they do not depend on others objects to exist. A heart still remains a heart even when it's removed from the body. It does not depend on the body to be a heart, nor does it depend on any other object to be what it is, namely a heart.
  • maximally self-connected and self-contained
    Self-connected and self-contained is the fact that all constituent parts are not separated from each other by spatial gaps as opposed to objectaggregate. [footnote MIE 2008]
  • independent of that of other entities
    This refers to the fact that the entity can exist without the need of other entities to exist, it exists 'on its own'. A rock still exists, even when it's moved elsewhere, it still is a rock. The rock does not need other rocks to exist 'as a rock', nor does it have to be in the dessert to 'be a rock'.
  • maintained through time
    Maintained through time refers to the fact if the entity exists, all parts of the entity also exist. In the case of a heart, this means that every entity of the heart (such as right ventricle, aorta, cardiac septem) all 'exist' when the heart 'exists'. A heart might be functioning today and not tomorrow, yet it still is the same heart.

Other Examples

  • A bus
  • An apple
  • A pencil
  • A cell
  • A lung
  • An organism
bfo:objectaggregate

Definition
A bfo:objectaggregate is a "snap:IndependentContinuant" ("independent_continuant") that is a mereological sum of separate "snap:Object" ("object") entities and possesses non-connected boundaries.

Example: a flock of geese

  • snap:IndependentContinuant and independent_continuant
    Both snap:IndependentContinuant and independent_continuant come from the terminology used in BFO. In this stage it is not important to know where they are referring to, but you can always check the [glossary] for more information.
  • a mereological sum of separate "snap:Object" ("object") entities
    The degree of unity of the objectaggregate is less than the object. In the case of a gooze vs a geeze, it should be clear that the unity is less strong for the flock of geese in comparison to a single goose. Also note, that an objectaggregate consists only out of snap:object, as in a flock of geese is a collection of multiple geese and nothing but geese.
  • non-connected boundaries
    Where the previous class stated that there were no spatial gaps between the different elements (e.g. in the case of a rock, there is no 'space' between the elements of the rock), this is not the case for an objectaggregate. There are gaps between all or some of its parts. In the example of a flock of geese, there is a gap between goose 1, goose 2, goose 3... (but not between the parts of a goose, which is a snap:object).

Other Examples

  • A heap of stones
  • A group of commuters on the subway
  • A collection of random bacteria
  • The patients in a hospital
  • symphony orchestra
bfo:faitObjectPart

Definition
A bfo:fiatObjectPart is a "snap:IndependentContinuant" ("independent_continuant") that is part of a "snap:Object" ("object") but is not demarcated by any physical discontinuities.

Example: the north east of Brussels

  • snap:IndependentContinuant and independent_continuant
    Both snap:IndependentContinuant and independent_continuant come from the terminology used in BFO. In this stage it is not important to know where they are referring to, but you can always check the [glossary] for more information.
  • part of snap:Object but not demarcated by physical discontinuities
    The boundaries between the different parts of an object are natural discontinuous, such as the natural discontinuity of the head of a goose and the neck. However for a Fiat part (cf. fiatObectPart), there is no such clear discontinuity. For the north east of Brussels, there is no clear distinguishable discontinuity, but nevertheless is a distinct part of Brussels. Therefore it goes within the class of snap:fiatObjectPart

Other examples

  • Upper and lower lobes of the left lung
  • The dorsal and ventral surfaces of the body
  • The east side of Saarbruecken
  • The lower right portion of a human torso
  • A fragment of bone
  • A pound of meat
  • A spherical mass of biomatter
  • A two inch wide slice cut from the chicken’s wing

Create a new class

  • Select the "Class" tab.

Selection of the class tab

  • Select the BFO class in the lef pane. Two options:
    • Process
    • Material Entity
Note: do not choose the classes Object, ObjectAggregate, FiatObjectPart. If it's an Object, ObjectAggregate, FiatObjectPart, then select 'Material Entity' as shown on the screenshot.



  • Click on 'Create Subclass' to create a new Subclass.
The class you're about to create will be automatically added to the Quick ID class.

Selection of the class "Process" and creating a new class

  • This should look like the screenshot on your right.

Result of the new created class

  • Name your class. Hint: this is most likely the name of your term. But do note that when adding the terms they must be annotated according to the OBI minimum metadata requirments.

Result of the new created class

Define the newly created class

Next you need to define the properties of your newly created class. Read through this section and go to the examples to get a better idea on what is expexted.
Fill in a single value for each of these properties (e.g. only 1 definition, 1 reference...). If you need/have multiple values for your class, use the option of adding an extra field (see "Add extra fields" at the end of this table on how to do that). This means that if you have multiple references for your definition (e.g. a wikipage and a book which are the sources of your definition), than add as many additional "definition source" as required. Follow the OBI minimum metadata guidelines for your values.

  • Define the property "example of usage"
    • Double click in Value field
    • Give an example of usage of your term, e.g. a title of an article using the actual term
  • Define the property "preferred term"
    • Double click in Value field
    • Fill in the name you'd prefer to give your term
  • Define the property "alternative term"
    • Double click in Value field
    • Fill in the name you'd prefer to give your term in the case the preferred term is not available
  • Define the property "preferred term"
    • Double click in Value field
    • Fill in the name you'd prefer to give your term

The properties pane

  • Define your definition
    • Double click in the Value field
    • If it's a process, use the following structure:
      "A [term] is a process that [description of what the process does] and has the input [material entity / information] and utilizes the function of a [material entity/device]. The output of the process is [material entity / information]. "
    • If it's a material entity, use the following structure:
      "A [term] is a material entity that [description of material]."
      If appropriate also add the following:
      "The [term] is manufactured by [organization or person], has function [function], has supplier [organization or person]."
  • Define the property "definition editor"
    • Double click in Value field
    • Fill in your name (since you are the editor of this term)
  • Define the property "definition source"
    • Double click in Value field
    • Fill in the source of the term's definition. This can be a wikipedia page, a book reference... Be precise in your reference.


  • Set the curation status to "uncurated".
    • In the right pane, just beneath the field where you named the class, click on the icon that says "Select existing resource..." (and not "Add existing resource as value..."
    • A popup screen will appear, and select uncurated in the right pane of the popup screen.
    • Click OK










    • The 'Value' of "has curation status" should now be uncurated

Result of the new created class

Result of the new created class

  • Add extra fields (if applicable): Sometimes you might need more than 1 field of a specific property to "fully" describe your term. This could be in the case of e.g. definition source (if you have more than 1 source that needs to be referred to), definition editor (if you're not the only one adding this term). Use common sense to evaluate how many additional fields you require (if any). When e.g. adding the definition source, only list the main references. There is no need to list all references used for the definition. This goes for all additional fields.
    If you need an additional field:
    • Click the icon "Create new annotation value"
    • Select the value you are after (e.g. an additional definition source)
    • NOTE: you can only create a new annotation value after you already filled in the value for that particular property. So fill in your alternative term first, then and only then you are able to create an additional alternative term.

Create a new annotation value by clicking the icon "Create new annotation value"

Check consistency

Submit to the OBI repository

Examples on how to define your term

The best way of getting an idea on how it's supposed to be done, is to browse the OBI repository (which you checked out using SVN). However, for you convenience we provide some examples of Protege both from Quick Terms as from OBI core terms. This will give an insight in how a Quick Term could look like and how a core term of OBI in its final form looks like. They main difference between such Quick Term and a core OBI term is the status of being uncurated as a Quick Term.
The following terms are snapshots and possibly due for change. The following term descriptions therefore are not necessarily the latest versions of the term within OBI. As said, for the latest versions do use Protege itself. They are merely provided as an easily accessible 'first glance' of the terms.

The terms are sorted according to the BFO class. The decision to rank them in e specific class are not describes in these examples. Such an explanation can be found in the explanation of the BFO classes.

Hence we end up with the following structure:

Visual Fixation

Can be found in the OBI at

  entity
  ⌊ occurent
    ⌊ processual entity
      ⌊ process
        ⌊ visual fixation


Properties and Values

Editor note

Not identical to "fixational eye movements" (or fixational instability, retinal jitter). Fixational eye movements refer to the movement (retinal jitter) of the eye during fixation. Fixation Task refers to the task to fixate a specific object and does not target the movement of the eye during this task.
More on fixational instability can be found here: http://en.wikipedia.org/wiki/Fixational_eye_movements

preferred term

visual fixation

alternative term

visual fixation task

Definition

A visual fixation is a process that maintains the visual gaze on a location or stimulus and has the input of visual stimulus (stimuli) and utilizes the function of an eye. The output of the process is the image which falls on the fovea of the eye.

Definition Editor

PERSON: Dirk Derom

Definition Source

http://en.wikipedia.org/wiki/Fixation_(visual)

Definition Source

http://www.encyclopedia.com/doc/1O87-visualfixation.html

Example of usage

"The monkey sat in a primate chair inside a sound-attenuated room with his head fixed. In the BST, the monkey was required to direct and maintain his gaze at a central fixation spot during a first fixation (‘pre-target’) period of 1.5 s." Lauwereyns, J., K. Watanabe, et al. (2002). "A neural correlate of response bias in monkey caudate nucleus." Nature 418(6896): 413-417

Example of usage

Munoz, D. P., I. T. Armstrong, et al. (2003). "Altered control of visual fixation and saccadic eye movements in attention-deficit hyperactivity disorder." J Neurophysiol 90(1): 503-14.

has curation status

uncurated

rdfs label

visual fixation


DNA sequence variation detection

Can be found in the OBI at

  entity
  ⌊ occurent
    ⌊ processual entity
      ⌊ process
        ⌊ DNA sequence variation detection


Properties and Values

Editor note

-

preferred term

-

alternative term

-

Definition

DNA sequence variation detection is a process which aims at finding changes (expansion, amplification, deletion, mutation) in sequence of DNA molecule.

Definition Editor

PERSON: Philippe Rocca-Serra

Example of usage

Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641

has curation status

metadata complete

rdfs label

DNA sequence variation detection


Storage

Can be found in the OBI at

  entity
  ⌊ occurent
    ⌊ processual entity
      ⌊ process
        ⌊ storage


Properties and Values

Editor note

-

preferred term

-

alternative term

-

Definition

storage is a process by which material entities are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability

Definition Editor

Philippe Rocca-Serra

Definition Source

OBI-Branch

Example of usage

PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.

has curation status

metadata complete

rdfs label

storage


Face

Can be found in the OBI at

  entity
  ⌊ continuant
    ⌊ independent continuant
      ⌊ material entity
        ⌊ face


Properties and Values

Editor note

-

preferred term

face

alternative term

-

Definition

The term face refers to the central sense organ complex, for those animals that have one, normally on the ventral surface of the head and can depending on the definition in the human case, include the hair, forehead, eyebrow, eyes, nose, ears, cheeks, mouth, lips, philtrum, teeth, skin, and chin.

Definition Editor

PERSON: Dirk Derom

Definition Source

http://en.wikipedia.org/wiki/Face

Example of usage

Farah, M. J. (1996). "Is face recognition 'special'? Evidence from neuropsychology." Behav Brain Res 76(1-2): 181-9.

has curation status

uncurated

rdfs label

face


Rat

Can be found in the OBI at

  entity
  ⌊ continuant
    ⌊ independent continuant
      ⌊ material entity
        ⌊ rat


Properties and Values

Editor note

-

preferred term

rat

alternative term

-

Definition

Rats are various medium sized, long-tailed rodents of the superfamily Muroidea. "True rats" are members of the genus Rattus, the most important of which to humans are the black rat, Rattus rattus, and the brown rat, Rattus norvegicus. Many members of other rodent genera and families are also called rats and share many characteristics with true rats.

Definition Editor

PERSON: Dirk Derom

Definition Source

http://en.wikipedia.org/wiki/Rat

Example of usage

Stalnaker, T. A., M. R. Roesch, et al. (2006). "Abnormal associative encoding in orbitofrontal neurons in cocaine-experienced rats during decision-making." Eur J Neurosci 24(9): 2643-53.

has curation status

uncurated

rdfs label

rat


Word

Can be found in the OBI at

  entity
  ⌊ continuant
    ⌊ independent continuant
      ⌊ material entity
        ⌊ word


Properties and Values

Editor note

-

preferred term

word

alternative term

-

Definition

A word is a unit of language that carries meaning and consists of one or more morphemes which are linked more or less tightly together, and has a phonetic value. Typically a word will consist of a root or stem and zero or more affixes.

Definition Editor

PERSON: Dirk Derom

Definition Source

http://en.wikipedia.org/wiki/Word

Example of usage

Pulvermuller, F., R. Assadollahi, et al. (2001). "Neuromagnetic evidence for early semantic access in word recognition." Eur J Neurosci 13(1): 201-5.

has curation status

uncurated

rdfs label

word


Cell Culture Supernatant

Can be found in the OBI at

  entity
  ⌊ continuant
    ⌊ independent continuant
      ⌊ material entity
        ⌊ cell culture supernatant


Properties and Values

Editor note

PRS:22022008: moved from _unclassified to _a defined class is needed following BM call

Editor note

PRS:22022008. result from protocol_application where input=cell culture and output=supernatant

preferred term

cell culture supernatant

alternative term

-

Definition

Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell.

Definition Editor

PERSON: Bjoern Peters

Definition Source

GROUP: IEDB

Example of usage

Solution containing RPMI, fetal calf sera, antibiotics, and monoclonal antibody UCHT1. Isolation of proliferation factor of immature T-cell clone in concanavalin A-stimulated splenocyte culture supernatant. Immunology. 2003 Jun;109(2):209-16. PMID: 12757615

has curation status

metadata complete

rdfs label

cell culture supernatant

Physical Document

Can be found in the OBI at

  entity
  ⌊ continuant
    ⌊ independent continuant
      ⌊ material entity
        ⌊ physical document


Properties and Values

Editor note

BP: moved and renamed for BFO

Editor note

information_content_entity "is_encoded_in" some physical_document in obi before split (040907).

preferred term

physical document

alternative term

-

Definition

A physical document is an object serving as a record of information by means of symbolic marks.

Definition Editor

PERSON: Bjoern Peters

Definition Source

GROUP: OBI

Example of usage

a book is a physical document

has curation status

metadata complete

rdfs label

physical document

Glossary of Common Terminology

Concept Origin Short Description Example

Span


BFO


Description of span


example

Snap

BFO

Description of snap

example

Quick Terms

OBI

Description of Quick Terms

example