Model: Types to consider

[maxkfranz]

A case that is commonly encountered in molecular biology articles is the description of interactions that occur within a sub-cellular compartment (e.g. nucleus) or near a cellular structure (e.g. plasma membrane). Furthermore, there are cases in which entities are involved in interactions that facilitate their movement from one location to another.

The issue here is to provide support for describing the sub-cellular location of an entity. This is also related to the issue of support for describing transport with respect to (sub-)cellular location.

Examples from Molecular Cell, 'Online Now' subset:

• Najafov et al. Molecular Cell, Volume 75, August 8, 2019, Pages 1-12
• Chino et al. Molecular Cell, Volume 74, June 6 2019, Pages 1-13
• Balsa et al. Molecular Cell, Volume 74, June 6 2019, Pages 1-14
• Ritchie et al. Molecular Cell, Volume 75, July 25 2019, Pages 1-10

[IgorRodchenkov]

Please stop opening new empty TODO issues like crazy 😜 It’s no good

IR

On Jun 18, 2019, at 3:16 PM, Max Franz notifications@github.com wrote:

TODO

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[jvwong]

Filtered GO Slim Generic for cellular_component

id	label	synonyms
http://purl.obolibrary.org/obo/GO_0005615	extracellular space	intercellular space
http://purl.obolibrary.org/obo/GO_0005737	cytoplasm
http://purl.obolibrary.org/obo/GO_0005856	cytoskeleton
http://purl.obolibrary.org/obo/GO_0005730	nucleolus
http://purl.obolibrary.org/obo/GO_0005576	extracellular region	extracellular
http://purl.obolibrary.org/obo/GO_0005575	cellular_component	"cell or subcellular entity,cellular component,subcellular entity"
http://purl.obolibrary.org/obo/GO_0005694	chromosome	"prophase chromosome,interphase chromosome,chromatid"
http://purl.obolibrary.org/obo/GO_0009536	plastid
http://purl.obolibrary.org/obo/GO_0005618	cell wall
http://purl.obolibrary.org/obo/GO_0005739	mitochondrion	mitochondria
http://purl.obolibrary.org/obo/GO_0005622	intracellular	"protoplasm,protoplast,nucleocytoplasm,internal to cell"
http://purl.obolibrary.org/obo/GO_0005623	cell
http://purl.obolibrary.org/obo/GO_0043226	organelle
http://purl.obolibrary.org/obo/GO_0005794	Golgi apparatus	"Golgi complex,Golgi,Golgi ribbon"
http://purl.obolibrary.org/obo/GO_0005840	ribosome	"free ribosome,ribosomal RNA,membrane bound ribosome"
http://purl.obolibrary.org/obo/GO_0005811	lipid droplet	"adiposome,lipid particle,lipid body"
http://purl.obolibrary.org/obo/GO_0005777	peroxisome	"peroxisomal,peroxisome vesicle"
http://purl.obolibrary.org/obo/GO_0005654	nucleoplasm
http://purl.obolibrary.org/obo/GO_0005773	vacuole	vacuolar carboxypeptidase Y
http://purl.obolibrary.org/obo/GO_0009579	thylakoid	photosynthetic membrane
http://purl.obolibrary.org/obo/GO_0032991	protein-containing complex	"protein-protein complex,protein complex,protein containing complex,macromolecule complex,macromolecular complex"
http://purl.obolibrary.org/obo/GO_0005815	microtubule organizing center	"MTOC,microtubule organising centre"
http://purl.obolibrary.org/obo/GO_0005783	endoplasmic reticulum	ER
http://purl.obolibrary.org/obo/GO_0031410	cytoplasmic vesicle	"cytoplasmic, membrane-bounded vesicle,cytoplasmic membrane-enclosed vesicle,cytoplasmic membrane bounded vesicle"
http://purl.obolibrary.org/obo/GO_0031012	extracellular matrix	"proteinaceous extracellular matrix,matrisome"
http://purl.obolibrary.org/obo/GO_0005829	cytosol
http://purl.obolibrary.org/obo/GO_0005635	nuclear envelope
http://purl.obolibrary.org/obo/GO_0005634	nucleus	"cell nucleus,horsetail nucleus"
http://purl.obolibrary.org/obo/GO_0030312	external encapsulating structure
http://purl.obolibrary.org/obo/GO_0000229	cytoplasmic chromosome	cytoplasmic interphase chromosome
http://purl.obolibrary.org/obo/GO_0000228	nuclear chromosome	nuclear interphase chromosome
http://purl.obolibrary.org/obo/GO_0005768	endosome
http://purl.obolibrary.org/obo/GO_0005886	plasma membrane	"juxtamembrane,cytoplasmic membrane,cell membrane,plasmalemma,bacterial inner membrane,inner endospore membrane,cellular membrane,plasma membrane lipid bilayer"
http://purl.obolibrary.org/obo/GO_0005764	lysosome
http://purl.obolibrary.org/obo/GO_0005929	cilium	"primary cilium,flagellum,eukaryotic flagellum,microtubule-based flagellum"

[jvwong]

A conversation with curator (SARS-Cov-2) regarding compartments:

There are some that wouldn’t need compartments, but I think for a good number it would be useful. The reaction I’d like to show is that the E protein of SARS CoV vreates a channel in the ERGIC and Golgi membranes and allows for Ca2+ flux into the cytosol. Similar reaction for Orf3a except it create K+ permeable channels.

[maxkfranz]

Possible compartment UIs:

(1) Compartments are drawn the same as complexes. It's very easy to draw, but it requires more disambiguation. They are disambiguated by name -- and potentially other widgets within the entity popover.

(2) Compartments are drawn as lines separating the screen, and position indicates whether a given entity is within a compartment. This is more complicated for users to draw, but it may be a more traditional view. With this approach, figures may not scale well to small sizes, e.g. for a tweet or thumbnail.

[jvwong]

Recent user feedback:

Once you click submit is that final and you can no longer make any additions for that paper?

Is it possible to explicitly specify the post-translational state of a protein (e.g. “monoubiquitinated FANCD2 interacts with DNA”)? I guess this can be done by labelling the complex (e.g. “ID2 complex with ubiquitin on FANCI(K523) and FANCD2(K561) interacts with DNA”) but is this against the spirit of the database?

Is it possible/worthwhile to have the option to draw the inhibition/activation arrows connecting to an interaction arrow, for example: “USP1 inhibits DNA binding of ID2 complex via deubiquitination of FANCD2”?

[jvwong]

from #989

Proposal is add additional selections for 'glycosylation/deglycosylation'.

Via author feedback:

... However, there was no glycosylation and deglycosylation subcategories under posttranslational modifications. These two are equivalent to phosphorylation and dephosphorylation. Moreover, although deglycosylation is not as common, glycosylation is likely to be the most common posttranslational modification in nature, with at least 50% and potentially up to 70% of proteins bearing glycans. Therefore, it might be good to consider adding glycosylation and deglycosylation as two subcategories of posttranslational modifications.

I have to mention that some types of glycosylation also occur co-translationally. However, to my knowledge, there is no type of glycosylation that exclusively occurs co-translationally (but not post-translationally). Therefore, it is fair to add the above-mentioned categories under posttranslational.

[jvwong]

An example of a disease entity 'abnormal mitral valve'

Hypothesis-free phenotype prediction within a genetics-first framework. Nat Comm. (2023)