Pathema

Key takeaways

Pathema belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Pathema to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Pathema from memory before moving on to harder problems.

Reference excerpt

Pathema was one of the eight bioinformatics resource centers funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institute of Health (NIH), which is an agency of the United States Department of Health and Human Services. Pathema was funded for five years from 2004 through a contract to The J. Craig Venter Institute, and is currently led by PI Granger Sutton. Pathema is the web resource for JCVI's NIAID-funded Bioinformatics Resource Center, and was one of eight such centers designed to support bio-defense and infectious disease research. The overarching goal of Pathema is to provide a core resource that will accelerated scientific progress towards understanding, detection, diagnosis and treatment of diseases caused by six clades of Category A-C pathogens (Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens, and Entamoeba histolytica) involved in new and re-emerging infectious diseases. Pathema provides comprehensive curated datasets for the targeted pathogen clades, along with advanced bioinformatics capabilities geared specifically towards biodefense requirements, and the identification of potential targets for vaccine development, therapeutics and diagnostics.

Supported Pathema organisms

Pathema analysis tools Pathema supports a suite of over 50 web-based single gene, whole-genome and multi-genome comparative tools to facilitate analyses of genomic sequence and annotation data of over 80 NIAID Category A-C prokaryotic pathogens. Tools available on the BRC resource are developed and customized to best meet the scientific needs of the pathogen research community based on feedback solicited through community outreach. Additionally, they are designed to facilitate scientific exploration in the areas of functional curation, pathogenicity, therapeutics, comparative analysis and functional genomics. While every tool has several applications, taken together they provides numerous opportunities for discovery and hypothesis generation. The suite of Pathema analysis tools include:

Over 25 different search capabilities allow users to mine and retrieve data stored in the BRC comparative database. Search tools query genes, genomes, sequences or text, matching user-defined strings across gene loci, gene symbols and protein product names. Other queries include EC#, GenBank, SwissProt, and GO id searches. Common sequence search methods such as BLAST, HMM and protein motif searches are also available. Over 20 different displays and analyses of whole-genome data. Whole-genome data can be displayed graphically as a linear representation of genes on regions of a chromosome or as a complete circle for an entire chromosome. Users can investigate biochemical pathways, codon usage tables, percent GC plots, computer generated 2D and restriction digest gels, and retrieve summary information such as average gene size or numbers of coding regions as viewable and downloadable tables and lists. Over 15 different comparative analysis tools. The basis for Pathema's comparative tools is either pre-generated protein clusters or All vs. All searches. Incorporated, are the most popular tools of the publicly available Sybil comparative analysis suite. Sybil uses pre-generated protein clusters as the underlying data for its synteny gradient and comparative genomic displays, with protein cluster ortholog, paralog and singleton data available to the user. Individual gene pages highlighting annotation data and associated evidence as well as single gene analysis tools. Annotation data displayed and downloadable includes product name, gene symbol, EC number, GO ids, functional role category assignment, DNA sequence and protein sequence. Calculating the TmHMM profile, secondary structure and third position GC-Skew are just a few types of analyses users can perform. Links to other relevant resources such as Swiss-Prot, GenBank, Prosite, Pfam, etc., are also available.

References

Brinkac LM, Davidsen T, Beck E, et al. (January 2010). "Pathema: a clade-specific bioinformatics resource center for pathogen research". Nucleic Acids Research. 38 (Database issue): D408–14. doi:10.1093/nar/gkp850. PMC 2808925. PMID 19843611. Greene JM, Collins F, Lefkowitz EJ, et al. (July 2007). "National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics". Infection and Immunity. 75 (7): 3212–9. doi:10.1128/IAI.00105-07. PMC 1932942. PMID 17420237.

External links Pathema Publications Pathema Presentations NIAID home page Bioinformatics Resource Centers The NIAID page describing the goals and activities of the BRCs PathogenPortal - A hub site for the BRCs; provides Summary information

Worked examples

Example 1 — a first encounter with Pathema

Start with the simplest possible case. Write down what Pathema claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Pathema before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Pathema ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Pathema

In research: Pathema appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Pathema in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Pathema is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics organizations, Biological databases, so understanding it makes those chapters shorter.
In everyday life: Look for Pathema outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

How to study Pathema in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Pathema means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Pathema out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Pathema in simple terms?

Pathema was one of the eight bioinformatics resource centers funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institute of Health (NIH), which is an agency of the United States Department of Health and Human Services. Pathema was funded for fi…

Why does Pathema matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Pathema?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Pathema.