Documentation for Protein-containing complex annotation for CoNECo

Named Entity Annotation

General guidelines

Entities that fall within the scope of the Gene Ontology term protein-containing complex are the target of named entity annotations for CoNECo.

Excerpt taken from Gene Ontology: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.

If a term is found in Gene ontology but it is NOT a protein-containing complex, then it will NOT be considered a Complex in this effort (e.g. ribosome).
There is a list of groups of Complexes which are protein-containing complex in GO, but will not be annotated as Complex in this effort. The list is in the end of the page.
Gene Ontology-Cellular Component (GO-CC) and specifically GO terms under protein-containing complex will be the target for Named Entity Normalization.
If a protein-containing complex can be identified as such by the annotators, but there is no entry in Gene Ontology corresponding to the entity then it will receive an annotation as a named entity (NE), but will not have a normalization to GO-CC.
The first resource that is trusted to resolve issues is Gene Ontology. If there is still not enough information there, inconsistencies will be resolved using Complex Portal, Reactome, CORUM, and as a last result the literature.

Annotation span

For each mention of a protein-containing complex (Complex hereafter) name, the annotation aims to mark the minimal span containing the full name of the entity mentioned in the text so that the marked span starts and ends on a boundary between an alphanumeric string and a non-alphanumeric character (e.g. space or hyphen). The following provides examples and guidelines for exceptional cases.

Modifiers and head words that are not part of the name are excluded from the annotated span, for example (annotated span in bold)

human NFkappaB complex
phosphorylated RNA polymerase II

This includes the word “complex” which should not be annotated as part of the entity.

Affixes and markers are similarly excluded from the annotation span even when they are part of the same syntactic word with a Complex name as long as there is a separating nonalphanumeric character, for example (annotated span in bold):

phospho-RNA polymerase II

However, annotation boundaries must coincide with the boundary between an alphanumeric and a non-alphanumeric character. In cases where a Complex name is written with one of the following regular affixes without such a boundary, the affix is included in the annotated span:

species identifier, e.g. h for human or m for mouse
p for phosphorylated
wt for wild-type
si for small interfering RNA
sh for small/short hairpin RNA
anti for antibody

Thus, for example (annotated span in bold):

the human complex hNFkappaB, and the murine complex mNFkappaB
pRNApolII (phosphor RNA polymerase II)

Specific rules for NER

When a protein-containing complex name coincides with the name of a GGP or the GGPs comprising it or the name of a Protein Family, separated by ANY punctuation, annotation of the Protein or Protein Family named entities is preferred over annotation of the protein-containing complex entity
ERMES complex (otherwise known as Mdm10/Mdm12/Mmm1 complex)

In the example above Mdm10/Mdm12/Mmm1 are not annotated as a single Complex entity, as they constitute three separate Protein NEs

Two notable exceptions are Arp2/3 and SWI/SNF where a single Protein-containing complex NE is annotated instead.

Annotations should be applied to all variants of a Complex name: e.g. NF kappaB, NF-kappaB, NFkappaB should all be marked as Protein-containing complex
PDB identifiers (e.g. 3BMP, 4BQ6) will NOT be annotated as Protein-containing complex even if when checked against PDB they correspond to one.

List of GO terms that will not be annotated as Complex

GO:1990104 DNA bending complex
GO:0140535 intracellular protein-containing complex
GO:1902494 catalytic complex
GO:0070069 cytochrome complex
GO:0031074 nucleocytoplasmic transport complex
GO:0005875 microtubule associated complex
GO:0001114 protein-DNA-RNA complex
GO:0150005 enzyme activator complex
GO:0019907 cyclin-dependent protein kinase activating kinase holoenzyme complex
GO:0044796 DNA polymerase processivity factor complex
GO:0098636 protein complex involved in cell adhesion
GO:0098635 protein complex involved in cell-cell adhesion
GO:0098637 protein complex involved in cell-matrix adhesion
GO:0043235 receptor complex
GO:0140368 decoy receptor complex
GO:1903768 taste receptor complex
GO:0098666 G protein-coupled serotonin receptor complex
GO:1990563 extracellular exosome complex
GO:0019036 viral transcriptional complex
GO:0098796 membrane protein complex
GO:0098803 respiratory chain complex
GO:1990684 protein-lipid-RNA complex
GO:1990686 LDL-containing protein-lipid-RNA complex
GO:1990685 HDL-containing protein-lipid-RNA complex
GO:0140513 nuclear protein-containing complex
GO:0035097 histone methyltransferase complex
GO:0000109 nucleotide-excision repair complex
GO:0008023 transcription elongation factor complex
GO:0005849 mRNA cleavage factor complex
GO:0000152 nuclear ubiquitin ligase complex
GO:0032994 protein-lipid complex
GO:0060987 lipid tube
GO:1990777 lipoprotein particle
GO:0030076 light-harvesting complex
GO:0098798 mitochondrial protein-containing complex
GO:0090665 glycoprotein complex
GO:1990351 transporter complex
GO:0005667 transcription regulator complex
GO:0017053 transcription repressor complex
GO:0090576 RNA polymerase III transcription regulator complex
GO:0090577 RNA polymerase IV transcription regulator complex
GO:0090578 RNA polymerase V transcription regulator complex
GO:1903865 sigma factor antagonist complex
GO:0000120 RNA polymerase I transcription regulator complex
GO:0090575 RNA polymerase II transcription regulator complex
GO:0032992 protein-carbohydrate complex
GO:0046806 viral scaffold
GO:0032300 mismatch repair complex
GO:0032993 protein-DNA complex
GO:0031588 nucleotide-activated protein kinase complex
GO:1990234 transferase complex
GO:0061695 transferase complex, transferring phosphorus-containing groups
GO:1902911 protein kinase complex
GO:0009365 protein histidine kinase complex
GO:1902554 serine/threonine protein kinase complex
GO:0000307 cyclin-dependent protein kinase holoenzyme complex
GO:1902554 nuclear cyclin-dependent protein kinase holoenzyme complex
GO:1902493 acetyltransferase complex
GO:0031248 protein acetyltransferase complex
GO:0031501 mannosyltransferase complex
GO:0106068 SUMO ligase complex
GO:1902503 adenylyltransferase complex
GO:0042575 DNA polymerase complex
GO:0030880 RNA polymerase complex
GO:0005965 protein farnesyltransferase complex
GO:0034708 methyltransferase complex
GO:1990228 sulfurtransferase complex
GO:0016459 myosin
GO:0045298 tubulin
GO:0031941 F-actin
GO:0005942 PI3K
GO:0000786 nucleosome
GO:0038201 mTOR
GO:0034360 chylomicron remnant
GO:0071256 translocon
GO:1990425 ryanodine receptor
GO:0034270 cytoplasm to vacuole targeting
GO:0106003 beta-amyloid

For information on Annodoc, see http://spyysalo.github.io/annodoc/.