8. BioSource

The BioSource is used for:

• Host Organism of the experiment

• Expressed in (Biosource used for expressing the participant)

• Interactor Organism: the Organism from which the interactor originates

A Biosource may be any of the following:

a) An organism (tissue/cell line unspecified) Example: Homo sapiens

b) A tissue type, which includes cell suspensions derived from tissues.

c) A cell line

d) in vitro

N.B. in the IntAct editor ‘Cell type’ denotes ‘Cell line’.

8.1. How to create a new BioSource/Host Organism

In practise this only needs to be done if an organism is not currently listed on the drop-down menu for “Host Organism” – most common organisms are already present.

From the publication or Experiment level, click on Main → New → Organism

The main source for organism information is http://www.uniprot.org/taxonomy/

Add the NCBI Tax Id of the new organism e.g. 40324 (for Stenotrophomonas maltophilia), and enter it in NCBI Tax Id field in the IntAct editor.

Press ‘Auto-complete’, and the other fields should be filled in. (short label is “stema” taken from the UniProt “Mnemonic”/5 letter organism identifier, and the UniProt Xref should have qualifier set as ‘identity’.)

Then Save.

8.2 How to create a Cell or Tissue Type

There are two stages to this:-

First, check the cell line or tissue is NOT present in the Biosource drop-down menu already - so SEARCH for it in the editor.

If the cell line/tissue is not currently present in the editor

Select Main → New → CV object/

Then Select ‘Cell Type’ or ‘Tissue’ – as appropriate

Click Create

Shortlabel: Add the name of cell line/tissue (in lowercase letters and using underscores instead of spaces)

Fullname: Repeat the name of cell line/tissue and add a very brief description

Then add an Xref or Annotation:

Tissue:

Database = “Brenda”

Identifier = “tissue identifier” (BTO:xxxxxxxx) or EFO

Qualifier = “Identity”

http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO

or

http://www.ebi.ac.uk/ols/ontologies/bto

or

http://www.uniprot.org/docs/tisslist.txt

Cell Type (immortalised cell line):

Cabri or other Database:

Database = “Cabri” or other appropriate DB

Identifier = “Cabri or other DB identifier”

Qualifier = “Identity”

ATCC cell lines:

Do NOT add as Xref, but

Annotation topic = “url”

Description = “url of entry”(if you cannot do either of these, add the catalogue number as a Annotation topic = “comment”.)

AND add an annotation (comment) giving further info about the cell line.

To locate your cell line in Cabri/ATCC it is probably easiest to do a Google search such as “293 cabri” or “293 atcc”.

Some cell lines are now present in Brenda.

Link this new cell type/tissue to a BioSource. If you do not, you will not be able to see it on the Host-Organism drop-down menu.

Select Main → New → Organism

Enter the TaxID of the species this cell line/tissue belongs to

Click on Auto Fill

Short-label: ‘Species-name of cell line/tissue’ e.g. ‘human-293. Use underscores instead of spaces in the cell type/tissue name.

Fullname: Repeat the name of cell line/tissue and add a very brief description, e.g. Human epitheloid cervix carcinoma HeLa cells.

Add either the Cell type (cell lines) OR Tissue (tissue or primary cells) from the drop-down list near the bottom of the page

NB: Start the species name with upper case, unless there's a good reason not to. Do not add a full-stop at the end of the full name.

Save

The new cell line/tissue should now appear on the Host organism drop-down menu and can be used in an experiment.

8.2.1 Tissues vs cell lines

There can be confusion as to what constitutes a ‘tissue’. For the purposes of the IntAct database, tissue includes primary cells which have been directly derived from an organism, then passaged to provide a single cell type. A ’tissue’ will usually have an entry in either the Brenda tissue ontology (https://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO or https://www.ebi.ac.uk/ols/ontologies/bto) or UniProtKB tissue list: http://www.uniprot.org/docs/tisslist.txt

When a specific cell type cannot be found in either list, use the closest term available and add the detailed description in the ‘exp-modification’ annotation on experiment.

Example: colonic circular smooth muscle – add as (Tissue) ‘circular smooth muscle’ and add ‘colon’ as an exp mod.

Examples: blood, aortic smooth muscle, adipocyte, melanoma, neuron

An embryo becomes a foetus when organogenesis commences and the dpc (days post coitum) of the organism should be considered when using these terms.

In the case of a specific bacterial strain, take the strain name from UniProtKB species list: http://www.uniprot.org/docs/speclist.txt or http://www.uniprot.org/taxonomy.

8.3 Cell Type

Immortalised cell lines are referred to as ‘cell types’ in IntAct.

8.3.1 Re-classified cell lines

If a cell line has been re-classified or proven to be contaminated it must be annotated to the corrected BioSource. Example: In EBI-367374 (PMID:15109305) the authors state that KB cells were used in the experiment. Subsequently these cells have been re-classified as a HeLa sub-clone (See definition in CABRI database). Therefore, the BioSource for this experiment must be entered as HeLa cells and a note in the annotation under ‘CAUTION’ to explain the discrepancy.

8.4 Special cases

In the case of host organism for Y2H assays, it was agreed to use the top level hierarchical yeast term (yeasx TaxID:4932), but if a yeast protein was identified as an interactor, this should be mapped to the correct strain or reference proteome.

In the case of a crystal, the host organism is always taken as the crystallisation solution i.e.’in vitro’ even in the case of a homomultimer.