Latest revision as of 18:20, 18 October 2013

Statement of Purpose

In an attempt to improve curation efficiency, provide distinct curation milestones, and create a common curation goal for curators, we would like to classify the C. elegans corpus into biologically relevant categories. These categories could represent different biological processes, molecular functions, anatomy terms, disease relevance, signaling pathways, phenotypes or any other categorical distinction we see as appropriate as we investigate this organizational scheme. This Wiki page is intended to collect and organize our thoughts and proposals as to how to best organize the C. elegans corpus (or for nematodes in general), including but not limited to:

What fundamental categories and/or hierarchies we can create to categorize papers
Methods or approaches for assigning individual papers to these categories
How we go about choosing a category as a curation priority
Determining what our goals should be for tackling a category or topic
Distributing the curation efforts among curators

Categorical Schemes

Categories could be devised or arranged in a number of ways. Current or proposed approaches include:

Using WormBook chapters as a basis for categories
Pathways (Wnt, MAPK, TGF, Ras, etc.)
Processes (Aging, Sex Determination, Meiosis)
Phenotypes
Commonly referenced gene sets
Topics commonly studied in C. elegans due to its advantages as a model system

Pilot Category Trees

WormBook Chapter categories

Genetics and Genomics

Genetics
- Complementation
- Essential genes
- Gene duplications and genetic redundancy
- Genetic enhancers
- Genetic mosaics
- Genetic suppression
- Karyotype, ploidy, and gene dosage
- Natural variation and population genetics
Genomics
- Network biology
- Noncoding RNA genes
- Genomic classification of protein-coding gene families
- Germline genomics
- Mitochondrial genetics
- Nematode genome evolution
- Gene structure
- Transposons

Developmental Control

Asymmetric cell division and axis formation in the embryo
The C. elegans intestine
The C. elegans pharynx: a model for organogenesis
Emrbyological variation during nematode development
Epidermal morphogenesis
Gastrulation in C. elegans
Hermaphrodite cell-gate specification
Notch signaling in the C. elegans embryo
Programmed cell death
Translational control of maternal RNAs

Signal Transduction

Protein Kinases
Canonical RTK-Ras-ERK signaling and related alternative pathways
Eph receptor signaling
Heterotrimeric G proteins
(Homologs of the) Hh signaling network
Notch signaling
Nuclear hormone receptors
Signaling in the immune response
Small GTPases
TGF-Beta signaling
Putative chemoreceptor families (in C. elegans)
Wnt signaling

Molecular Biology

Micro RNAs
Noncoding RNA genes
DNA repair
Gene expression changes associated with aging
Genomic classification of protein-coding gene families
Germline chromatin
Mechanisms and regulation of translation
Gene structure
Pre-mRNA splicing and its regulation
RNA-binding proteins
Roles of chromatin factors in development
Transcription mechanisms
Transcriptional regulation of gene expression
Translational control of maternal RNAs
Trans-splicing and operons
Transposons
Ubiquitin-mediated pathways
X-chromosome dosage compensation

Post-embryonic Development

Dauer
Evolution of development in nematodes related to C. elegans
Gene expression changes associated with aging
Hermaphrodite cell-gate specification
Male development
The measurement and analysis of age-related changes
Morphogenesis of the vulva and the vulval-uterine connection
Roles of chromatin factors in development
Vulval development

Neurobiology and Behavior

Behavior
- Feeding
- Egg-laying
- Male mating behavior
- Learning and memory
Development
- Neurogenesis
- Synaptogenesis
- Glia
Function
- Potassium channels
- Putative chemoreceptor families (in C. elegans)
- Sensory cilia
Neurotransmitters
- Acetylcholine
- Biogenic amine neurotransmitters
- Ethanol
- GABA
- Ionotropic glutamate receptors: genetics, behavior, and electrophysiology
- Neuropeptides
Sensory modalities
- Chemosensation
- Mechanosensation

Biochemistry

Ascaroside signaling
Carbohydrates and glycosylation
Intermediary metabolism
The eggshell in the C. elegans oocyte-to-embryo transition
Mitochondrial Unfolded Protein Response (UPR)
Model animals for the study of oxidative stress from complex II
Reproduction, fat metabolism, and life span: what is the connection?
A worm rich in protein: Quantitative, differential, and global proteomics

Sex Determination

Hermaphrodite cell-gate specification
Male development
Morphogenesis of the vulva and the vulval-uterine connection
Sex determination in the germ line
Somatic sex determination
The evolution of nematode sex determination
Vulval development
X-chromosome dosage compensation

Evolution and Ecology

Nematode diversity and phylogeny
Ecology of Caenorhabditis species
Evolution of development in nematodes related to C. elegans
The evolution of nematode sex determination
Interactions with microbial pathogens
Molecular evolution inferences from the C. elegans genome
Natural variation and population genetics
Nematode genome evolution
The phylogenetic relationships of Caenorhabditis and other rhabditids
Genomics and biology of the nematode Caenorhabditis briggsae
The biology and genome of Heterorhabditis bacteriophora
Oscheius tipulae
Pristionchus pacificus
Strongyloides spp.
Biology and genome of Trichinella spiralis

Cell Biology

Asymmetric cell division and axis formation in the embryo
Autophagy
Basement membranes
The cadherin superfamily
Carbohydrates and glycosylation
Cell cycle regulation
Cell division
Cell fusions
The cuticle
Epidermal morphogenesis
Epithelial junctions and attachments
Gastrulation in C. elegans
Intracellular trafficking
Mitochondrial genetics
Potassium channels
Programmed cell death
Sarcomere assembly in C. elegans muscle
Sensory cilia
Sperm motility and MSP
Spermatogenesis
Synaptogenesis

The Germ Line

Control of oocyte meiotic maturation and fertilization
Germline chromatin
Germline genomics
Germline proliferation and its control
Germline survival and apoptosis
Specification of the germ line
Spermatogenesis

Disease Models and Drug Discovery

C. elegans and volatile anesthetics
Anthelmintic drugs
Obesity and the regulation of fat metabolism

Ad hoc category trees

Biological Processes

Development
- Development by stages
  - Germline development
  - Embryonic development
  - Larval development
  - Aging
- Development by tissue
  - Ectoderm development
    - Nervous system development
    - Epithelial system development
  - Mesoderm development
    - Muscle development
  - Endoderm development
    - Intestine development
Cell Biological Processes
- Cell Cycle
  - Mitosis
  - Meiosis
Behavior
- Chemotaxis
- Thermotaxis
- Touch response
- Mating
Gene Expression
- Transcription and its regulation
- Post-transcriptional regulation
- Translation and its regulation
- Post-translational regulation

Pathways

Wnt signaling
TGF signaling
Insulin-like signaling
Ras signaling

Biological Entities

Anatomy terms
Genomic elements
- Genes
  - Coding genes
    - Genes by protein domain
    - Genes by protein complex
  - Non-coding genes
- Regulatory elements
Cellular components
- Nucleus
- Plasma membrane
- Endosome
- Lysosome
- Endoplasmic reticulum
- Golgi apparatus
- Cytoskeleton
- Mitochondria

Stress categories

Stress

Stress Types
- Chemotoxic/Xenobiotic stress
- Desiccation, Dehydration
- Electrophilic stress (lipoperoxidation, 4-hydroxynonenal (4-HNE))
- Genotoxicity, DNA damage, Replicative stress
- Glucose stress
- Heavy metals
- Injury/Trauma
- Ischemia
- Mechanical stress
  - Shear stress
- Metabolic/metabolite stress
- Misfolded/Unfolded protein stress, Proteotoxicity, Endoplasmic reticulum (ER) stress, Mitochondrial (mit) stress
  - Beta-amyloid aggregation
  - Polyglutamine aggregation
- Mitochondrial stress
- Osmotic, Salt, Hypertonic stress
- Oxidative stress, Hypoxia/Anoxia, Hyperoxia
  - Reactive Oxygen Species (ROS)
  - Peroxides
- Pathogen stress (a whole field)
- Starvation
  - Glucose, ATP depletion
- Thermal stress (heat/cold shock)
- UV, Gamma, X-Ray irradiation
Stress Topics
- Hormesis
- Stress fibers
- Stress granules
- Stress response
  - Mitochondrial stress response
- Stress tolerance/resistance
  - Stress adaptation
  - Thermotolerance
Stress reporters
- Pgst-4::GFP
- Phsp-4::GFP
- Phsp-16.2::GFP
- Psod-3::GFP

Methods & Approaches for Paper Categorization

Collecting (manually) lists of relevant keywords, and performing (manual) Textpresso or PubMed searches
Running Textpresso scripts
- SVM-based, supervised vs. unsupervised, keywords
- Requires positives and negatives for training
- Chris is in the process of assembling all WormBook articles for an initial training round
Collecting common keywords from papers in out Author First Pass list of papers
- Yuling has run scripts to determine word frequencies among these papers

Choosing a Curation Priority

Once we are satisfied with a categorization scheme(s), we may want to select a single category for curators to focus their efforts. Our criteria for choosing a category may depend on a number of factors:

Number of papers in each data type backlog
Number of papers in a category
Distribution of data types (or required curator effort) for papers in a category
Current representation of category topic in WormBase
- Highly represented: we may want to "polish off" what we have to generate a complete picture
- Lowly represented: May be low-hanging fruit for covering new topics
Current representation of gene function for genes represented in category
- We could focus on genes with little or no known function

See the Topic Curation page

Goals for a Curation Milestone

Some goals that have been discussed are:

Completing curation backlog for all data types for a given category
Completing curation of human disease-relevance for a given category
Generating (or filling out) a WormBase Process page and WikiPathway
Goals could be set for each curation upload (every ~two months)
We can post the results of the milestone on the WormBase homepage/blog

Distributing Curation Efforts

@@ Line 261: / Line 261: @@
 Stress
 *Stress Types
-**Dessication, Dehydration
+**Chemotoxic/Xenobiotic stress
+**Desiccation, Dehydration
 **Electrophilic stress (lipoperoxidation, 4-hydroxynonenal (4-HNE))
-**Heat Shock/Stress
+**Genotoxicity, DNA damage, Replicative stress
+**Glucose stress
 **Heavy metals
+**Injury/Trauma
 **Ischemia
-**Misfolded/Unfolded protein stress
+**Mechanical stress
+***Shear stress
+**Metabolic/metabolite stress
+**Misfolded/Unfolded protein stress, Proteotoxicity, Endoplasmic reticulum (ER) stress, Mitochondrial (mit) stress
 ***Beta-amyloid aggregation
 ***Polyglutamine aggregation
+**Mitochondrial stress
 **Osmotic, Salt, Hypertonic stress
 **Oxidative stress, Hypoxia/Anoxia, Hyperoxia
 ***Reactive Oxygen Species (ROS)
 ***Peroxides
+**Pathogen stress (a whole field)
 **Starvation
-**UV irradiation
+***Glucose, ATP depletion
+**Thermal stress (heat/cold shock)
+**UV, Gamma, X-Ray irradiation
 *Stress Topics
 **Hormesis
+**Stress fibers
+**Stress granules
 **Stress response
+***Mitochondrial stress response
 **Stress tolerance/resistance
-**Stress granules
+***Stress adaptation
+***Thermotolerance
 *Stress reporters
 **Pgst-4::GFP
-**Phsp-16::GFP
+**Phsp-4::GFP
+**Phsp-16.2::GFP
 **Psod-3::GFP
@@ Line 311: / Line 326: @@
+See the [[Topic_Curation|Topic Curation]] page
 = Goals for a Curation Milestone =

Difference between revisions of "WormBase Paper Categorization"