annotation_rules.md

Annotation guidelines

This document outlines the guidelines for manually annotating entities in scientific texts related to molecular simulations.

Molecule: MOL

Definition

The MOL entity covers molecular compounds, including simple molecules, ions, nucleic acids, proteins, lipids, sugars, polymers, and complexes. MOL entities should be uniquely identifiable.

Rules

1. Exclude whitespace and punctuation marks around entities
2. The molecule name should be at least 2 characters long
3. Treat singular and plural forms equivalently and annotate both (e.g., alkane and alkanes)
4. Annotate chemical formulas and abbreviations separately from full molecule names.
5. Include amino acid and nucleic acid sequences
6. Include any identifiers (PDB ID, UniProt ID...)
7. Exclude adjectives or descriptors that modify the molecule (e.g., hydrated, charged, folded, tetrameric)
8. Exclude generic terms like protein, lipid, phospholipid, DNA, sugar, water, alcohols, ions, compounds...
9. Exclude specific residues or domains like Lys-353...
10. Annotate individual components of a molecular complex or mixture separately, excluding connectors (/, -) and generic assembly terms (complex, dimer, mixture).

Good examples

• sodium chloride
• ethanol
• ammonia
• Q29537
• 2RH1
• Na⁺
• carbon
• L-alanine
• POPC

Bad examples

• H (Rule 2)
• coronavirus 2019-nCoV protease Mpro (annotate separately coronavirus 2019-nCoV protease and Mpro, Rule 4)
• hydrated sodium chloride (only annotate sodium chloride, Rule 7)
• lipids (Rule 8)
• DNA (Rule 8)
• binding protein (Rule 8)
• ions in solvent (Rule 8)
• TLR4/MD-2 complex (annotate TLR4 and MD-2 separately, Rule 10)

Force field and model: FFM

Definition

The FFM entity refers to any force field or molecular model used to describe the interactions between particles in a simulation. This includes all classical all-atom force fields, coarse-grained models, solvent models, and water models. Both the name and version of the force field/model are relevant and should be annotated when available.

Rules

1. Include water models and other specific solvent models (e.g., TIP3P, SPC/E).
2. Exclude generic terms like force field or model.
3. Include the force field name when directly combined with a specific water or solvent model as a single block (e.g., CHARMM TIP3P).

Good examples

• CHARMM36
• CHARMM C36m
• AMBER99SB
• GROMOS53a6
• GROMOS96 43A1
• Poger GROMOS 53A6_L
• TIP3P
• charmm36 (v. june 2015)

Bad examples

• TIP3P water (only annotate TIP3P) (Rule 1 and Rule 2)
• the force field (Rule 2)
• the CHARMM36 force field (only annotate CHARMM36) (Rule 2)
• CHARMM TIP3P water model (only annotate CHARMM TIP3P, Rule 2 and Rule 3)

Software name: SOFTNAME

Definition

The SOFTNAME entity refers to the name of any software used for molecular simulation, visualization, or analysis. It includes packages for molecular dynamics, modeling, trajectory processing, and any other computational tasks relevant to the simulation workflow.

Rules

1. Exclude generic words such as software, tool, or program unless they are part of the official name.
2. Exclude algorithms like SHAKE, RESP...
3. Exclude programming languages like Python, C++, Fortran...

Good examples

• GROMACS
• VMD
• NAMD
• PyMOL
• PLUMED
• COLVAR
• CHARMM-Gui
• Jupyter
• Autodock
• CHARMM
• AMBER22

Bad examples

• the simulation software (Rule 1)
• GROMACS software (only annotate GROMACS, Rule 1)
• Anton (it is a supercomputer, not a software, Rule 1)
• SHAKE (it is an algorithm, not a software, Rule 2)
• Python (Rule 3)

Software version: SOFTVERS

Definition

The SOFTVERS entity refers to the version identifier of any software used in the simulation process. It includes version numbers, release tags, or labels, regardless of formatting (e.g., numeric, date-based, semantic).

Rules

1. Must follow a corresponding SOFTNAME entity (software/tool name)
2. Keep numeric and symbolic parts intact (e.g., 1.2.3-beta)
3. Include any suffixes (e.g., 2020.4), prefixes (e.g., v5.1.2)
4. Exclude surrounding words like version, release, software...

Good examples

• v5.0
• 2020.4
• 5.1.4

Bad examples

• charmm36 (v. june 2015) (it is not a software version, Rule 1)
• software (v. 2016.4) (only annotate v. 2016.4) (Rule 3 and Rule 4)
• release 2023.1 (only annotate 2023.1) (Rule 4)
• latest version (too generic, Rule 4)

Simulation time: STIME

Definition

The STIME entity refers to the duration for which a production molecular dynamics simulation is run.

Rules

1. Exclude minimization or equilibration time or any analysis time. Only annotate the production simulation time.
2. If simulation time is presented as a range (e.g. 3 × 200ns), annotate only the simulation time (e.g. 200ns)
3. Exclude vague expressions like several hours or long simulations

Good examples

• 200ns
• 50 picoseconds
• 100 ns
• 4-8 μs
• 10 to 50 ns
• Microsecond

Bad examples

• 10–50 replicas (not a simulation time)
• 100 ns of equilibration (not a production simulation time, Rule 1)
• 3 × 200ns (only annotate 200ns, Rule 2)
• for several hours of computation (too vague, Rule 3)

Simulation temperature: STEMP

Definition

The STEMP entity refers to the thermal conditions under which a simulation is conducted. It includes any explicitly stated temperature values, with or without units.

Rules

1. Do not annotate temperatures reported as experimental measurements, observed values, or results. Only annotate temperatures that define or control the simulation conditions
2. The unit is not mandatory, but the context must unambiguously indicate that the number refers to temperature used as simulation conditions
3. Exclude surrounding words like temperature of or heated to
4. Include room temperature or body temperature

Good examples

• 300K
• 500 degrees Celsius
• 298 (Rule 2)
• room temperature (Rule 4)

Bad examples

• "measured as a function of temperature" 293.15–313.15 K (not a simulation temperature, Rule 1)
• "temperature of fusion" 70°C (not a simulation temperature, Rule 1)
• heated up (too generic, Rule 3)
• at low temperature (too generic, Rule 3)