Project-specific Terms

This is a glossary of biological terms used in PiMS.

Administrator

The administrator is a special user who is the only user defined when you first install PIMS. The administrator has the right to create new users, user groups, and information owners and also specifies the access rights that apply for the user groups and information owners.

Annotation

In PiMS a file which is attached to a record is referred to as an 'Annotation'. You may add annotations to Target, Experiment, Protocol and Citation records.

Barcode

PIMS will generate barcodes to use as unique identifiers for samples, reagents etc., which can be affixed to sample containers.
A scanning device (barcode reader), linked to PIMS, will enable the user to identify the sample and hence simplify the completion of a data-input form.
If a sample or reagent arrives in the laboratory with an existing bar code (the supplier's product code), this should be replaced with a PIMS barcode which will identify the sample as unique.
However, where a supplier's barcode is a unique identifier e.g. a barcode on a certain types of 96-well plates or on a plate of user-defined PCR primers, this barcode can be used.

Blueprint component

A 'wish target', domain or fragment of a 'wish target', DNA, RNA, poly- or olio-saccharides or a small molecule ligand or co-factor.
Part of an Experiment Blueprint

Citation

In PIMS a citation is a record of the details which describe a literature reference such as a book, conference, journal or thesis. The details might include a title, author(s), year of publication, page numbers, PubMed Id., etc. Some details might be specific to the type of citation, for example a book citation might also include the publisher and ISBN. Where the literature reference is stored electronically, a link to the file can also be recorded with the citation.

Conforming sample

All batches of the same reagent can share reagent reference data. Similarly, reference data for the same reagent from different suppliers, or different grades of a reagent will have some details in common. This might include hazard information, sample categories to classify the reagent etc. Where a reagent uses PIMS reference data in this way it is referred to as a conforming sample in the sense that it "conforms to " a reference sample. For example, all batches of Sodium chloride from Sigma-Aldrich or from Fischer Scientific would conform to the same reference sample for a generic sodium chloride reagent.

Construct

A DNA molecule created from fragments. Typically a plasmid or vector with an "insert" of foreign DNA. The insert is often generated by the polymerase chain reaction (PCR) but can also be produced by restriction enzyme digestion of a larger piece of DNA.
See also Polycistronic construct

Container / Holder

A sample or reagent will be held in a container e.g. a tube, well, plate etc.
In addition, several containers might be grouped together such as the wells in a 96-well plate. In this case the plate is termed a holder.
A holder may also hold other holders e.g. a rack of plates.
Commonly used containers and holders can be selected from lists in PIMS which can be added to.

Creator

The person e.g. the Scientist, who is responsible for, or who "created" a particular item in PIMS. Typically relates to Experiments, Protocols and Targets.

Crystallisation space

The physico-chemical and protein-specific parameters which define the conditions in a crystallisation well
may include:

• pH
• temperature
• concentration of various salts, precipitants, buffers, additives etc.
• drop size
• protein concentration
• presence/absence of co-factors or ligands

These can be thought of as the co-ordinates in a multi-dimensional space.
In a typical crystallisation experiment, the number of dimensions will be approximately 100.
The probability of a crystallisation well yielding crystals, for a particular protein will vary with movement through this space.

DbRef (Database reference)

In PIMS a reference to information stored in a remote database is called a DbRef or Database reference.
To create a DbRef you need to record the name of the database, e.g. Swiss-Prot and the unique identifier for the database record, e.g. P49650. Typically such a reference will be created when an appropriate PIMS record is being edited and a link to the record will be cretaed automatically.

Drug target

A protein or protein complex which is implicated in a disease and so has the potential to be affected by a specific drug.

Experiment Blueprint (the name may be changed)

The term Experiment Blueprint is a description of a clearly defined experimental objective i.e. what you plan to work on.

It describes any particular combination of one or more 'wish targets', domains or fragments of 'wish targets', DNA, RNA, poly- or olio-saccharides or any small molecule ligand or co-factor that you intend to study.
For example, the components of a macromolecular complex, although there will often be only one component.
Each of these components is defined as a Blueprint component.

When you record the details for an experiment in PIMS, the experiment is linked to the Target via an Experiment Blueprint.

Examples of an Experiment Blueprint might be:
a protein, a protein-DNA complex, a multi-protein complex or a protein comlexed with a ligand or co-factor.

In addition, multiple Experiment Blueprints can de defined from a single 'wish target' illustrating the fact that different domains or fragments of the 'wish target' may be studied in various contexts.

For example: a given protein may have more than one distinct domains such as a kinase with catalytic and regulatory domains.
You may intend to study different aspects of the protein and so separate Experiment Blueprints might be:

• the full length protein
• the kinase domain
• the regulatory domain
• a complex between the two domains
• a complex including a substrate

In addition, an Experiment Blueprint might contain Blueprint components defined from separate Experiment Blueprints.
For example: an Experiment Blueprint, called AB1, describes an oligomeric protein AB with two subunits A and B.
This Experiment Blueprint will, therefore contain two Blueprint components A' and B', defined from thier respective 'wish targets' A and B.
A different Experiment Blueprint, AB2, describes the AB complex with a co-factor C bound.
In this case, there might be three Blueprint components A', B' and C' where C' is defined from a separate Experiment Blueprint C.

Express (exprimer)

To make protein from a gene.

Extinction Coefficient

The extinction coefficient (E) of a protein is an indicator of how much light it absorbs at a particular wavelength.
The molar extinction coefficient is a measure of the amount of light absorbed by a 1M solution in a pathlength of 1cm at a given wavelength.
This is a useful parameter for determining the concentration of a protein for example, during its purification.

The (molar) extinction coefficient of a protein can be estimated from a knowledge of its amino acid composition. The calculation is based on the number of tyrosine, tryptophan and cystine residues it contains using the known molar extinction coefficients of these residues.
The calculation forms part of the ExPASy ProtParam tool

E (protein) = no. Tyr x E (Tyr) + no. Trp x E(Trp) + no. Cys x E(Cys)
The absorbance of the protein can then be calclated:
Absorbance(protein) = E(protein) / Molecular weight

GMO

Genetically Modified Organism. A target protein is produced by adding the gene for it to a suitable organism, often E.Coli.

Genomic project

A means of grouping targets which are being studied together. The targets might be selected from one organism, or might belong to a particular class of proteins. You can define Genomic projects in whatever way is suitable for your method of working. For example, a Genomic project may correspond to a particular collaboration or a particular grant.

Homologous sequence

Protein, or nucleotide sequences are likely to be homologous if they show a "significant" level of sequence similarity. Truely homologous sequences are related by divergence from a common ancestor gene. Sequence homologues can be of two types:
(i) where homologues exist in different species they are known as orthologues. e.g. the α-globin genes in mouse and human are orthologues.
(ii) paralogues are homologous genes in within a single species. e.g. the α- and β- globin genes in mouse are paralogues

Input

An experimental product or stock material which is utilised in an experiment, one of a list of materials or ingredients. This may be a reagent or a sample created from a previous experiment.

Insert

A fragment of DNA, such as the product from a PCR reaction or one of the products from a restriction enzyme digest, which is 'inserted' into a vector.

Instrument

Details of the type(s) of laboratory equipment required for a protocol. Can include name, model, serial number etc.

Isoelectric point

The Isoelectric point or pI of a protein is the pH at which the net charge of the protein is neutral. i.e. the protein carries no net charge since it has an equal number of positive and negative charges. At pH values greater than the pI, a protein will carry a net positive charge. Similarly, at pH values less than the pI, a protein will carry a net negative charge.
Knowlede of a protein's pI is important for purification since it is the pH at which the protein will be at its least soluble.
The pI of a protein can be determined experimentally by isoelectric focussing (IEF) but the value obtained is often inaccurate since it is influenced by post translational modifications of the protein.
The theoretical pI can be calculated from the amino acid sequence of the protein, and there are a number of websites which provide this service. For example, see ExPASy's Compute pI/Mw tool.

Lab book (le cahier de manipulation)

A scientst's personal record of experiments planned and performed. The traditional way of managing laboratory information.

LIMS

Laboratory Information Management System

Location

An area in the laboratory, which you may wish to record as the location of a sample.
Examples are a fridge, a freezer, a freezer compartment or a room.

Molecular Component

PIMS defines a pure component with a known chemical structure, such as 'Sodium chloride', as a Molecular Component.
Restriction enzymes, constructs and primers are also examples of Molecular Components with additional characteristics.
Molecular Components are distinct from other components classified as 'Substance' 'Cell' and 'Composite'.

Molecule

In PIMS the term molecule is used to describe any type of pure component with a known chemical structure. This includes chemicals, DNA, RNA and proteins.

A target is associated with a protein molecule, and usually with one or more nucleic acid molecules. Once you have begun the protein production process, you may record information about the molecular components in your samples. Information that can be recorded about the actual molecules can include post-translational modifications.
A molecule can also be recorded for a chemical or reagent.

Optimisation

A further screening experiment, after an initial screening has indicated the approximate conditions for success. The screen used for optimisation will be customised in the light of the results of the screening experiment. How best to do this is a topic for research. Analysis of the records of past experiments (data mining) will facilitate this research.

Output sample

An experiment may or may not produce one or more output samples.

Owner

Each piece of information recorded in PIMS has an "owner". This may be for example a project group, or an external customer of the laboratory. The owner of a piece of information must be specified when it is first recorded.

Parameter

A value recorded for an experiment as defined by a Parameter definition in a protocol

Parameter definition

Protocol or experimental details may be documented by creating 'Parameter definitions'.
Examples of the use of Parameter definitions might include possible options for the set up of an experiment, e.g. whether or not a culture is to be shaken, or details which describe an experimental result.

Parameter definitions can be used to describe numerical or text values, a list of possible values, a checkbox for True/False values or to create a link to an image or experimental data file.

In a protocol you can define any number of Parameter definitions or experimental details which are variable e.g. a reaction temperature. When you create an experiment, the specific values for each parameter definition are recorded as a parameter.

Permission

An access permission is the right for the members of a user group to perform a certain operation on pieces of information owned by a specific owner: view, update, delete or create the information. PIMS keeps an audit trail, so that when information is updated or deleted, the previous version can still be viewed.

Plate (la plaque)

A holder with multiple wells (usually 24, 96, or 384), each capable of containing a sample.

Protein species

A term used to describe a protein or proteins of unknown function. For example a protein(s) identified only as a band(s) on a gel. Also used to describe the existence of previously undetected variants of a protein, such as alternative forms with different or post-translational modifications.

Polycistronic

Clusters of bacterial genes encoding proteins which are part of the same metabolic pathway are often arranged in tandem along the chromosome. They are transcribed as a unit from a single promoter resulting in the production of a single "polycistronic" messenger RNA (mRNA) which is subsequently translated into the proteins. An example is the E.coli Lac operon which consists of 3 genes required for the metabolism of galactose.
By contrast the majority of eukaryotic mRNAs are "monocistronic" and are translated only into a single polypeptide chain or protein. However, the chloroplasts of plants contain polycistronic mRNAs.

Polycistronic construct

See construct. A construct for the co-expression of multiple DNA fragments or genes. It can be used to express several recombinant proteins under the control of a single promoter. Analogous to a bacterial operon. This approach may be necessary in order to produce a soluble protein complex.

Protocol (le protocole)

A laboratory method, Standard Operating Procedure, or protocol. In PIMS, a protocol is represented as a series of steps which can be grouped into one or more procedures.

A procedure for carrying out an experiment.

Rack (l'etagere)

A holder capable of containing several plates.

Reference data

When PIMS is installed, it contains information about Chemicals, Database names, Hazard phrases, etc. This reference data can be read by any PIMS user, but can be updated only by the administrator.

Reagent information which is common to all batches of the same reagent. This can include supplier and safety information and also details for linking to the supplier's data sheet. It also indicates the appropriate sample category or categories.

Refinement

See optimisation.

Research target

A protein, protein complex or other molecular species whose function and/or structure is under investigation in a research environment.

Result

An experimental "result", examples include a value, set of values or a gel image, all of which provide information to the scientist.

Sample (l'echantillon)

A physical sample in a laboratory, produced by an experiment. Might also be referred to as an aliquot. Experiments utilise "input" samples and most create "output" samples. A sample may have one or more known sample components (des composants).

Targets and blueprint components have hypothetical molecules; samples have actual molecules.
The sequence of a target can be redefined as hypotheses develop whereas the sequence of a molecule in a sample may have to be corrected after new observations are made.
A sample has a particular location but the location of a target (or Experiment Blueprint) is the location of the output sample from the most recent successful experiment.

Sample category

Each sample or reagent can belong to one or more categories, e.g. buffer, salt, detergent, antibiotic, etc.

Sample component

A sample is made up of one or more sample components.
For example, a PCR buffer may contain three sample components: KCl, Tris and MgCl₂, each at a known, final concentration in the sample.
In PIMS, a sample component can be one of the following types:
Substance, Molecular component, Cell or Composite

Scale-up

v. or n. To perform an experiment in bulk, after the optimal conditions have been determined by a screening experiment.

Scientific Goal

The scientific goals of the project are the areas where PIMS can help scientists manage experimental and target information. They represent a means of grouping use cases based on perceived project needs, as defined in the project proposal and from requirements gathering. For certain scientific goals, the use of PIMS might influence laboratory practice. For example, the introduction of barcoding to facilitate sample tracking.

A scientific goal is what Alistair Cockburn calls a strategic scope, summary goal.

Screen

i. To perform a screening experiment.

n. A range of reagents (or samples mixed from standard reagents) prepared for use in a screening experiment, one for each constituent experiment.

Screening Experiment

There are situations where the appropriate reagents and/or conditions to use for a particular experiment have not been established. To resolve this problem, it is necessary to perform one or more experiments simultaneously, where the conditions and/or reagents are varied systematically in order to define a range of favourable combinations. The outcome of such a primary screen will help to define a narrower range of conditions for either optimisation or scale-up.

Stock solution

A Stock solution is a solution of a laboratory reagent of known, standard concentration. It is typically the highest concentration of the reagent kept in the laboratory. A stock solution may be purchased from a supplier or prepared in the laboratory. Typically a more dilute solution, a working dilution, will be used directly in experiments.

Substance

A substance is a component where no detailed chemical structure is provided such as 'salt' or 'phosphate'. This is also a simple way to describe complex mixtures, such as an extract or serum.

Target

Something that is or could be represented by a record in TargetDB.

The product of a gene (ORF). A target may be associated with the scientist who selected it.
PIMS can also record potential targets which have not yet been selected.

Target status

The stage a target (or experiment blue print) has reached in the protein production and crystalization process. This represents the most recent successful experiment. The possible statuses are the "Progression stages" defined by TargetDB:

Selected, PCR, Cloned, Expressed, Soluble, Scale-up, Purified, In crystallization, Crystallized, Diffraction-quality Crystals, Native diffraction-data, Phasing diffraction-data, HSQC, NMR Assigned, NMR NOE, Crystal Structure, NMR Structure, In PDB, Molecular Function, Biological Process, Cellular Component, Work Stopped, Other

User

Every operation performed with PIMS is part of a session which began by logging on with a specific user name. Each PIMS user has specific rights to view and update the laboratory information.

When you define a new project, you can also specify which PIMS users are participants in it.

User group

Users are grouped together to give them permissions for PIMS activities. Each user may be a member of several groups. For example at Alice and Bob may be members of the "Yeast" group, and are able to record new experiments on the yeast proteome. Alice may also be a member of the "Professors" group, and is able to view all information in the laboratory PIMS.

Value

The actual experimental value which relates to a parameter recorded for a protocol

Vector

A DNA molecule, containing regulatory sequences and coding seqences, into which a fragment of foreign DNA is inserted. The inserted fragment is referred to as the 'insert'.