> For the complete documentation index, see [llms.txt](https://intact-portal.gitbook.io/intact-portal-doc/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://intact-portal.gitbook.io/intact-portal-doc/docs/curation-manual/biosource.md).
# 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
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”
or
or
*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 ( or ) or UniProtKB tissue list:
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: or [http://www.uniprot.org/taxonomy](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](http://www.ebi.ac.uk/intact/search/do/hvWelcome?searchString=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.