WormBase Paper Categorization

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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:

  1. What fundamental categories and/or hierarchies we can create to categorize papers
  2. Methods or approaches for assigning individual papers to these categories
  3. How we go about choosing a category as a curation priority
  4. Determining what our goals should be for tackling a category or topic
  5. 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