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Sleep apnea occurs when breathing stops for brief periods of time while a person is sleeping. It can last for 10-30 seconds, and may occur up to 20-30 times per hour. During 1 night of sleep, this can cause up to 400 episodes of interrupted breathing.
There are three types of respiratory events:
- Obstructive apnea—caused by a temporary, partial, or complete blockage of the airway
- Central apnea—caused by a temporary failure to make an effort to breathe
- Mixed apnea—a combination of the first 2 types
Risk Factors
Sleep apnea is more common in men and in adults over 40 years of age.
Factors that increase your chances of developing sleep apnea include:
- Overweight
- Large neck circumference
- Family history of apnea
Structural abnormalities of the nose, throat, or other part of the respiratory tract. Examples include:
- Polyps
- Severely enlarged tonsils
- Deviated nasal septum
- Hypothyroidism
- Asthma
- Certain medications, such as sedatives and sleeping aids
- Alcohol consumption
- Smoking
Symptoms may include:
- Fatigue and sleepiness during waking hours
- Loud snoring
- Breathing that stops during the night—as noticed by a bed partner
- Repeated waking at night
- Unrefreshing sleep
- Morning headaches
- Poor concentration or problems with memory
- Irritability or short temper
People with chronic, untreated sleep apnea may be at risk for:
- Motor vehicle accidents
- Depression
- Hypertension
- Heart disease
- Stroke
- Kidney disease
An overnight sleep study is used to help diagnose sleep apnea.
Overnight Sleep Study (Polysomnography)
This test helps detect the presence and severity of sleep apnea. During sleep, it measures your:
- Eye and muscle movements
- Brain activity using an electroencephalogram
- Heart rate
- Breathing pattern and depth
- The percent of your red blood cells that are saturated with oxygen
Other Studies
In addition to sleep studies, your doctor may order:
- Blood tests to check thyroid function
- Electrocardiogram
- Pulmonary function tests
There are a number of treatment options for sleep apnea, including:
Behavioral Therapy
- Lose weight if you are overweight.
- Avoid using sedatives, sleeping pills, alcohol, and nicotine, which can make the condition worse.
- Try sleeping on your side instead of on your back.
- Use pillows to increase your level of comfort when sleeping.
- For daytime sleepiness, practice safety measures, such as avoiding driving or operating potentially hazardous equipment.
Mechanical Therapy
Continuous positive airway pressure (CPAP) is done by wearing a mask over your nose and/or mouth during sleep. An air blower forces enough constant and continuous air through your air passages to prevent the tissues from collapsing and blocking the airway.
Oral Appliances
Oral appliances that help keep the tongue or jaw in a more forward position may help those with mild to moderate sleep apnea. They can also be used for those with severe obstructive sleep apnea who cannot use CPAP therapy or have tried it without success.
In some cases, surgery may be advised. It is most often helpful in children.
Types of surgery that may be done to treat severe cases of sleep apnea include:
- Adenotonsillectomy—The adenoids and tonsils are removed.
- Uvulopalatopharyngoplasty—Excess soft tissue is removed from the nose and/or throat.
- Maxillomandibular advancement—The jawbone is repositioned forward.
- Tracheotomy —For life-threatening cases of sleep apnea, an opening is made in the windpipe to allow for normal breathing.
Bariatric surgery may help with weight loss in some people who are obese . This surgery may reduce many of the complications that are related to obesity, including sleep apnea.
Only used in central apnea, acetazolamide may help improve the ability to regulate breathing.
Supplemental oxygen may be given if blood levels of oxygen fall too low during sleep, even after opening the airway.
You may be able to prevent sleep apnea by maintaining a healthy weight . Avoid alcohol, nicotine, and sedatives, which may contribute to airway obstruction.
Revision Information
- Reviewer: Adrienne Carmack, MD
- Review Date: 01/2015 -
- Update Date: 08/11/2015 -


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© 2015 Specialized Bicycle Components. All rights reserved.
Emily Murphy does plenty for others. She does motherhood and a garden business. Coaching and chauffering. And then she does something fast, dirt-ridden and gritty for no one but herself: a few hours of pure, unadulterated escapism.
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Jessica Kuo needed a catharsis. After losing a friend to cancer, she climbed on a bike, started riding, and stopped when she got to the other side of the United States. She isn't an Olympian, she isn't made of steel. She is a woman who found therapy in the saddle of a bike.
Sophie Ballo had no choice but to cheat on running. The pavement pounding of too many marathons had taken its toll on her body, so friends convinced her to take up riding. She no longer cheats on running. It's not cheating when you take a job at Specialized and become one of the fastest riders in the building. It's called commitment.
Denise Bannert didn't do as she was told. When she was raised in the German flatlands, she moved to the mountains. When friends stuck to the road, she left for the trail. When it came time to stay indoors at a numbing desk job, she came to Specialized and did just the opposite.

subset: commoncrawl


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Phylo cookbook
m (→Index clades by name)
EricTalevich (Talk | contribs)
(→Convert to a PyCogent tree: Added DendroPy example)
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See the rpy2 documentation for further guidance.
See the rpy2 documentation for further guidance.
===Convert to a PyCogent tree===
===Convert to a PyCogent tree===
The tree objects used by Biopython and PyCogent are different. Nonetheless,
The tree objects used by Biopythonand PyCogent are different. Nonetheless, toolkits support the Newick file format, so interoperability is straightforward at that level
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===Convert to a NumPy array or matrix===
===Convert to a NumPy array or matrix===
Latest revision as of 03:04, 7 December 2013
Here are some examples of using Bio.Phylo for some likely tasks. Some of these functions might be added to Biopython in a later release, but you can use them in your own code with Biopython 1.54.
Convenience functions
Get the parent of a clade
The Tree data structures in Bio.Phylo don't store parent references for each clade. Instead, the
get_path method can be used to trace the path of parent-child links from the tree root to the clade of choice:
def get_parent(tree, child_clade): node_path = tree.get_path(child_clade) return node_path[-2] # Select a clade myclade = tree.find_clades("foo").next() # Test the function parent = get_parent(tree, myclade) assert myclade in parent
Note that
get_path has a linear run time with respect to the size of the tree -- i.e. for best performance, don't call
get_parent or
get_path inside a time-critical loop. If possible, call
get_path outside the loop, and look up parents in the list returned by that function.
Alternately, if you need to repeatedly look up the parents of arbitrary tree elements, create a dictionary mapping all nodes to their parents:
def all_parents(tree): parents = {} for clade in tree.find_clades(order='level'): for child in clade: parents[child] = clade return parents # Example parents = all_parents(tree) myclade = tree.find_clades("foo").next() parent_of_myclade = parents[myclade] assert myclade in parent_of_myclade
Index clades by name
For large trees it can be useful to be able to select a clade by name, or some other unique identifier, rather than searching the whole tree for it during each operation.
def lookup_by_names(tree): names = {} for clade in tree.find_clades(): if clade.name: if clade.name in names: raise ValueError("Duplicate key: %s" % clade.name) names[clade.name] = clade return names
Now you can retrieve a clade by name in constant time:
tree = Phylo.read('ncbi_taxonomy.xml', 'phyloxml') names = lookup_by_names(tree) for phylum in ('Apicomplexa', 'Euglenozoa', 'Fungi'): print "Phylum size", len(names[phylum].get_terminals())
A potential issue: The above implementation of lookup_by_names doesn't include unnamed clades, generally internal nodes. We can fix this by adding a unique identifier for each clade. Here, all clade names are prefixed with a unique number (which can be useful for searching, too):
def tabulate_names(tree): names = {} for idx, clade in enumerate(tree.find_clades()): if clade.name: clade.name = '%d_%s' % (idx, clade.name) else: clade.name = str(idx) names[clade.name] = clade return names
Calculate distances between neighboring terminals
Suggested by Joel Berendzen
import itertools def terminal_neighbor_dists(self): """Return a list of distances between adjacent terminals.""" def generate_pairs(self): pairs = itertools.tee(self) pairs[1].next() return itertools.izip(pairs[0], pairs[1]) return [self.distance(*i) for i in generate_pairs(self.find_clades(terminal=True))]
Test for "semi-preterminal" clades
Suggested by Joel Berendzen
The existing tree method
is_preterminal returns True if all of the direct descendants are terminal. This snippet will instead return True if any direct descendent is terminal, but still False if the given clade itself is terminal.
def is_semipreterminal(clade): """True if any direct descendent is terminal.""" for child in clade: if child.is_terminal(): return True return False
In Python 2.5 and later, this is simplified with the built-in
any function:
def is_semipreterminal(clade): return any(child.is_terminal() for child in clade)
Comparing trees
- Symmetric difference / partition metric, a.k.a. topological distance (Robinson-Foulds)
- Quartets distance
- Nearest-neighbor interchange
- Path-length-difference
Consensus methods
- Majority-rules consensus
- Strict consensus
- Adams (Adams 1972)
- Asymmetric median tree (Phillips and Warnow 1996)
Rooting methods
The basic method on the Tree class (not TreeMixin) is
tree = Phylo.read('example.nwk', 'newick') print tree # ... tree.root_with_outgroups({'name': 'A'}) # Operates in-place print tree
Normally you'll want the outgroup to be a monophyletic group, rather than a single taxon. This isn't automatically checked, but you can do it yourself with the
is_monophyletic method.
To save some typing, try keeping the query in a separate list and reusing it:
outgroup = [{'name': taxon_name} for taxon_name in ('E', 'F', 'G')] if tree.is_monophyletic(outgroup): tree.root_with_outgroup(*outgroup) else: raise ValueError("outgroup is paraphyletic")
- Root at the midpoint between the two most distant nodes (or "center" of all tips)
- Party tricks with
draw_graphviz, covering each keyword argument
Exporting to other types
Convert to an 'ape' tree, via Rpy2
The R statistical programming environment provides support for phylogenetics through the 'ape' package and several others that build on top of 'ape'. The Python package rpy2 provides an interface between R and Python, so it's possible to convert a Bio.Phylo tree into an 'ape' tree object:
import tempfile from rpy2.robjects import r def to_ape(tree): """Convert a tree to the type used by the R package `ape`, via rpy2. Requirements: - Python package `rpy2` - R package `ape` """ with tempfile.NamedTemporaryFile() as tmpf: Phylo.write(tree, tmpf, 'newick') tmpf.flush() rtree = r(""" library('ape') read.tree('%s') """ % tmpf.name) return rtree
See that it works:
>>> from StringIO import StringIO >>> from Bio import Phylo >>> tree = Phylo.read(StringIO('(A,(B,C),(D,E));'), 'newick') >>> rtree = to_ape(tree) >>> len(rtree) 3 >>> print r.summary(rtree) Phylogenetic tree: structure(list(edge = structure(c(6, 6, 7, 7, 6, 8, 8, 1, 7, 2, 3, 8, 4, 5), .Dim = c(7L, 2L)), tip.label = c("A", "B", "C", "D", "E"), Nnode = 3L), .Names = c("edge", "tip.label", "Nnode" ), class = "phylo") Number of tips: 5 Number of nodes: 3 No branch lengths. No root edge. Tip labels: A B C D E No node labels. NULL >>> r.plot(rtree)
See the rpy2 documentation for further guidance.
Convert to a DendroPy or PyCogent tree
The tree objects used by Biopython, DendroPy and PyCogent are different. Nonetheless, all three toolkits support the Newick file format, so interoperability is straightforward at that level by writing to a temporary file or StringIO object with one library, then reading the same string again with another.
from Bio import Phylo import cogent Phylo.write(bptree, 'mytree.nwk', 'newick') # Biopython tree ctree = cogent.LoadTree('mytree.nwk') # PyCogent tree
import dendropy # Create or load a tree in DendroPy dtree = dendropy.Tree.get_from_string("(A, (B, C), (D, E))", "newick") dtree.write_to_path("tmp.nwk", "newick", suppress_rooting=True) # Load the same tree in Biopython bptree = Phylo.read("tmp.nwk', 'newick')
Convert to a NumPy array or matrix
Adjacency matrix: cells are 1 (true) if a parent-child relationship exists, otherwise 0 (false).
import numpy def to_adjacency_matrix(tree): """Create an adjacency matrix (NumPy array) from clades/branches in tree. Also returns a list of all clades in tree ("allclades"), where the position of each clade in the list corresponds to a row and column of the numpy array: a cell (i,j) in the array is 1 if there is a branch from allclades[i] to allclades[j], otherwise 0. Returns a tuple of (allclades, adjacency_matrix) where allclades is a list of clades and adjacency_matrix is a NumPy 2D array. """ allclades = list(tree.find_clades(order='level')) lookup = {} for i, elem in enumerate(allclades): lookup[elem] = i adjmat = numpy.zeros((len(allclades), len(allclades))) for parent in tree.find_clades(terminal=False, order='level'): for child in parent.clades: adjmat[lookup[parent], lookup[child]] = 1 if not tree.rooted: # Branches can go from "child" to "parent" in unrooted trees adjmat += adjmat.transpose return (allclades, numpy.matrix(adjmat))
Distance matrix: cell values are branch lengths if a branch exists, otherwise infinity. (This plays well with graph algorithms.)
import numpy def to_distance_matrix(tree): """Create a distance matrix (NumPy array) from clades/branches in tree. A cell (i,j) in the array is the length of the branch between allclades[i] and allclades[j], if a branch exists, otherwise infinity. Returns a tuple of (allclades, distance_matrix) where allclades is a list of clades and distance_matrix is a NumPy 2D array. """ allclades = list(tree.find_clades(order='level')) lookup = {} for i, elem in enumerate(allclades): lookup[elem] = i distmat = numpy.repeat(numpy.inf, len(allclades)**2) distmat.shape = (len(allclades), len(allclades)) for parent in tree.find_clades(terminal=False, order='level'): for child in parent.clades: if child.branch_length: distmat[lookup[parent], lookup[child]] = child.branch_length if not tree.rooted: distmat += distmat.transpose return (allclades, numpy.matrix(distmat))
- Use an OrderedDict for
allclades, so the separate dictionary
lookupisn't needed. (Python 2.7+)
- Use NumPy's record array to assign clade names to rows and columns of the matrix, so
allcladesisn't needed either. (This works nicely along with the
tabulate_namesfunction given earlier.)
- Relationship matrix? See Martins and Housworth 2002


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Australian Bureau of Statistics
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Eels release Chris Sandow
THE Parramatta Eels have today agreed to release Chris Sandow effective immediately, pending lodgement with the NRL.
Warriors v Sea Eagles preview
JACK Clifton gives his thoughts on this weekend's meeting between the New Zealand Warriors and the Manly-Warringah Sea Eagles at Mt Smart Stadium.
Tigers v Roosters preview
JACK Clifton previews the upcoming clash between the Wests Tigers and the Sydney Roosters at ANZ Stadium.
Broncos v Titans preview
ROB Crosby looks at Friday's game between the Brisbane Broncos and the Gold Coast Titans at Suncorp Stadium.
In The Spotlight - Round 20
IT'S happening folks. The cream of the NRL crop are starting to rise to the top.
Team List Tuesday - Analysis Round 20
SAM Bourke is back with an analysis of all the team lists from round 20 - bringing you the ins and outs, and SuperCoach studs and duds to help you keep up to date.
LeagueUnlimited VB NSW Cup Teams - 2015 Round 20
ALL the teamlists and officials for Round 20 of the VB NSW Cup competition, with thanks to the NSWRL.com.au media team.
LeagueUnlimited SS Teams - 2015 Round 19
HERE are all the teams for Round 19 of the Sydney Shield thanks to the NSWRL
LeagueUnlimited ISC Teams - 2015 Round 20
ALL the teamlists and officials for Round 20 of the Intrust Super Cup competition, thanks to the Queensland Rugby League!
LeagueUnlimited RMC Teams - 2015 Round 19
HERE are the teams for Round 19 of the Ron Massey Cup thanks to the NSWRL.
LeagueUnlimited NYC Teams - 2015 Round 20
IT'S Teamlist Tuesday for Round 20 of the 2015 Holden Cup Under 20's Season! Around 5pm AEDT every Tuesday, the teams for each NYC round will be posted right here!
LeagueUnlimited NRL Teams - 2015 Round 20
IT'S Teamlist Tuesday for Round 20 of the 2015 NRL Season! Around 5pm AEDT every Tuesday, the full teams for each NRL round will be posted right here!
Memorable Debuts - Round 20
WELCOME to Memorable Debuts, a feature of LeagueUnlimited.com where we take a look at the upcoming matches of the round and see which players debuted in the same game all those years ago.
The Prism - Round 20 2015
VOX looks at the hottest topic in Rugby League at the moment - the division (or lack of division) between on-field and off-field persona. He also suggests his predictions, which based on past performance are probably a good bet...
The Synopsis - NRL Round 19
IN case you missed any of the action from round 19 of the NRL, George Peterson is on hand to bring you up to date which an overview of every game.


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These handouts provide facilitators with tools to implement the DPP intervention using strategies to achieve nutrition, physical activity and weight loss goals. En español
Diabetes Prevention Program (DPP)
This guide contains easy-to-understand charts and worksheets to help you track your diabetes health and work with your doctor to develop a plan to maintain a healthy heart. It is available in English and Spanish. En español
American College of Physicians (ACP)
This website is filled with information about living with diabetes and developing habits for healthy eating and physical activity through small, sensible steps. En español
This comprehensive guide will help you control your diabetes by keeping a balance between what you eat, your physical activity, and your medication. It will also help you take important steps to prevent diabetes-related health problems. En español
Centers for Disease Control and Prevention (CDC)
This bilingual Spanish and English presentation flipchart makes it easy to educate Hispanic and Latino Americans about the link between diabetes and heart disease. It includes easy-to-understand illustrations, a scripted presentation, and two copier-ready handouts. En español
National Diabetes Education Program (NDEP)
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Degrees and Certificates
Skyline College makes it possible to achieve all of your educational goals. Whether you are interested in automotive technology, accounting, computers or cosmetology, business or biomanufacturing — or even if you're not sure what you want to do — we have certificate and degree programs that can lead to a successful, productive and fulfilling future. You will benefit from Skyline College's individualized attention and an extensive array of student support services. Which of our programs is right for you?
Interdisciplinary Studies: Arts & Humanities Skyline PatternBelow are listed the courses you need to take to complete your degree or certificate program.
Requirements below should be used as a guide only. Current students should consult DegreeWorks for their specific requirements based on their catalog rights.
View key gainful employment outcomes for graduates from Skyline College's certificate programs, including estimates of the costs of tuition, books and supplies, and fees; average student loan debt; and normal time to completion of the certificate.


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Customer Reviews for Blackout Opaque / Blackout Window Shades
"Very pleased"
By Kari from NJ
We bought these blinds for our basement. They were very easy to install and look beautiful. They have a very high quality feel. I would definitely recommend these blinds to anyone.View this product
By pj from texas
Came in a timely manner and looks great on my windows. Much better than white blindsView this product
This item has been successfully added to your cart. Proceed to checkout or continue shopping.


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In an effort to keep residents and other interested persons informed wherever they may be, the City of Cambridge now offers free smartphone applications that help residents report public works issues like potholes and graffiti, access public safety news and information, and submit crime and other tips to police.
Click the links below to download the mobile applications offered by the City of Cambridge:
Cambridge iReportSubmit reports of potholes, rodents, un-shoveled sidewalks and more directly to City departments from your mobile device.More information
CodeRED Mobile AlertReceive emergency notifications from the City about snow emergencies, evacuations, and large-scale water outages or other service disruptions.More information
Cambridge Police MyPDSubmit crime tips to police, share feedback, ask questions, and access news and alerts.More information
CPD Tips AppSend anonymous crime tips to police from your iPhone, iPad and iPod Touch.
795 Massachusetts Ave
Cambridge MA, 02139
Ph: 617-349-4000
Monday: 8:30am-8pm
Tuesday-Thursday: 8:30am-5pm
Friday: 8:30am-12pm
Richard C. Rossi
City Manager
Lisa C. Peterson
Deputy City Manager


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- INTERPOL Lagos
Member since :
10 October 1960
Back to Africa
The Nigeria Police Force
To serve and protect
The Nigeria Police Force (NPF) is the principal law enforcement agency in Nigeria with a strength of more than 350,000 men and women. NPF is a federal Police force covering all 36 Nigerian states and the federal capital territory, Abuja.
- Protection of lives and property;
- Prevention, detection and investigation of crime;
- Prosecution of offenders.
- Administration and Finance;
- Operations;
- Works and logistic;
- Investigations;
- Training;
- Planning, Research and Statistics.
INTERPOL Lagos
The INTERPOL National Central Bureau (NCB) for Nigeria has two hubs:
- Abuja Office;
- Lagos Office.
Abuja is the administrative seat of the NCB, whilst the Lagos office is the operational hub. INTERPOL Lagos acts as the coordinating and liaison office between Nigerian law enforcement agencies and the INTERPOL community.
Partner agencies
Other key security agencies in Nigeria that work with the Nigeria Police include, but are not limited to:
National Drug Law Enforcement Agency
- Prevention and investigation of drug trafficking in Nigeria;
Economic and Financial Crimes Commission
- High profile, economic and financial crime;
Nigeria Immigration Services
- Regulation of immigration issues
- Coordination of travel document issues
- Extradition (in partnership with NPF);
Nigeria Customs Service
- Works with police at the border and entry points to check for smuggling and transborder crimes;
National Agency for Prohibition of Traffic in Persons
- Prevention of human being smuggling
- Prevention of forced labour;
National Agency for Foods, Drugs Administration and Control
- Regulation and control of food products and pharmaceutical products.
INTERPOL Lagos in action
03 November 2015
Réseau de trafiquants de véhicules dans les mailles de la police togolaise grâce à coopération policière INTERPOL
LOME (Togo) – Dans le cadre d'une opération policière menée par la Police Nationale du Togo contre le trafic régional de voitures volées et avec le concours des Bureaux Centraux Nationaux (BCN) d'INTERPOL du Benin, Cote d'Ivoire, Mali, Nigeria et Togo, le 21 juillet 2015 quatre véhicules ont été retrouvés, huit suspects arrêtés dans différents pays et un...
31 July 2015
Strengthening West African border security focus of INTERPOL programme
ABIDJAN, Côte d'Ivoire – Strengthening border management was the focus of a specialized INTERPOL course for immigration and customs officers from key border control points and National Central Bureaus across West Africa.During the two-week (20 – 31 July) course hosted by the INTERPOL Regional Bureau for West Africa in Abidjan, participants received in-dep...
22 May 2015
INTERPOL training in Ghana aims to strengthen regional police capacity in border management
ACCRA, Ghana – Law enforcement officers from across West Africa have received specialized training as part of an INTERPOL programme aimed at building policing capacity to strengthen border management.The two-week course (11 – 22 May) at the Kofi Annan International Peace Keeping Centre (KAIPTC) in Accra brought together 22 law enforcement officers from im...
16 July 2014
INTERPOL Nigeria escorts Nyanya bombing suspect extradited from Sudan
LYON, France – One of the suspected masterminds behind the April bombing of a bus terminus in Nyanya, Nigeria, Aminu Sadiq Ogwuche, has been extradited from Sudan with a police escort from INTERPOL Nigeria.Ogwuche, an alleged Boko Haram member faces charges including preparing, placing and detonating a vehicle-borne improvised explosive device which resul...
21 May 2014
'Wave of violence' in Nigeria condemned by INTERPOL Chief
LYON, France – INTERPOL Secretary General Ronald K. Noble has condemned the recent 'callous' violence in Nigeria which has seen at least 118 people killed in bombings in Jos on Tuesday, and many more fatalities during attacks in the north of the country.With the second bombing in Jos targeting rescue workers as they went to help the victims of the first b...
14 April 2014
INTERPOL condemns Abuja terror 'slaughter'
LYON, France – INTERPOL Secretary General Ronald K. Noble has condemned in the strongest terms the 'mass murder' of dozens of commuters after bomb explosions rocked a crowded bus station on the outskirts of Abuja on Monday.Officials said at least 70 people were killed and more than 120 injured."This slaughter of innocent members of the public will have ap...
24 January 2014
WAPIS office opens at ECOWAS headquarters in Abuja
ABUJA, Nigeria – As part of ongoing efforts to boost information exchange among law enforcement in West Africa, this week INTERPOL, in collaboration with the European Union and of the Economic Community of West African States (ECOWAS), opened an office for its West African Police Information System (WAPIS) programme in Nigeria.Located at the ECOWAS headqu...
11 October 2013
Corruption, financial crime and asset recovery focus of INTERPOL meeting in Nigeria
ABUJA, Nigeria – Senior investigators and prosecutors from West, East and Central Africa have come together in Nigeria to discuss ways to successfully identify, investigate and prosecute cases of corruption and related financial crimes at the 6th INTERPOL Global Programme on Anti-Corruption, Financial Crimes and Asset Recovery.Organized by INTERPOL's Anti...
19 June 2012
INTERPOL's largest operation combating illegal ivory trafficking targets criminal syndicates
LYON, France – INTERPOL's largest ever transnational operation targeting criminal organizations behind the illegal trafficking of ivory has resulted in more than 200 arrests and the seizure of nearly two tonnes of contraband elephant ivory.The three-month long Operation Worthy, which involved 14 countries across Eastern, Southern and Western Africa also r...
26 August 2011
INTERPOL condemns fatal bombing of United Nations building in Nigeria
LYON, France – INTERPOL Secretary General Ronald K. Noble has condemned today's attack on the United Nations compound in Abuja, Nigeria which has left at least 16 people dead and many more wounded.Secretary General Noble said the full resources of the world's largest police organization were at the disposal of the Nigerian authorities investigating the ca...
05 March 2010
INTERPOL co-ordinated operation targets illegal trade in wildlife medical products
LYON, France - An international operation co-ordinated by INTERPOL targeting the illegal trade in traditional medicines containing protected wildlife products has resulted in a series of arrests worldwide and the seizure of thousands of illegal medicines worth more than EUR 10 million.National wildlife enforcement authorities, police, customs and speciali...
17 February 2009
ABUJA, Nigeria – An agreement between Nigeria, Italy and INTERPOL has been signed in the Nigerian capital to strengthen co-operation in the fight against illegal immigration and human trafficking and to target the organizations behind these crimes.Co-ordinated under the auspices of INTERPOL, the two-year pilot project will see both countries' police force...
Red Notices 31
HENRY IFEANYI Age today: 41 years old
Nationality: Nigeria
HENRY IFEANYI Age today: 41 years old
Nationality: Nigeria
PAUL EJIKE Age today: 40 years old
Nationality: Nigeria , Sierra leone
PAUL EJIKE Age today: 40 years old
Nationality: Nigeria , Sierra leone
Yellow Notices 6
DEBBY Age today: 24 years old
Nationality: Nigeria
DEBBY Age today: 24 years old
Nationality: Nigeria
IKEGWURU Age today: 50 years old
Nationality: Nigeria
IKEGWURU Age today: 50 years old
Nationality: Nigeria
- 11th African Regional Conference - 1991 - Lagos
- 2nd African Regional Conference - 1965 - Lagos


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The MILLY collection epitomizes bold, advanced contemporary fashion with a feminine edge. Designer and founder Michelle Smith transforms classics by merging American sportswear silhouettes with distinctive Parisian atelier techniques. Smiths eye for impeccable detail, use of luxurious, cutting-edge fabrics and precise tailoring have made MILLY a cult favorite across the globe.
If an item you would like to purchase is out of stock, you can place a Special Order Inquiry. REVOLVE will then check the availability and obtain an approximate arrival date for the item, if available. Typically, it takes up to 3-4 weeks to verify this information.
Placing a Special Order Inquiry is absolutely free and there is no obligation to follow through with a purchase.
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A summary of results from Round 11 of the 20th First Utility Super League season, Europe's premier club rugby league competition.
LeagueUnlimited SS Teams - 2015 Round 7
ALL the teamlists and officials for Round 7 of the Sydney Shield are in, thanks to the media team at NSWRL.com.au!
LeagueUnlimited VB NSW Cup Teams - 2015 Round 8
ALL the teamlists for Round 8 of the VB NSW Cup competition, with thanks to the NSWRL.com.au media team.
Armchair Expert - Round 7
THE Armchair Expert is back for round 7. This week, Sam Flanagan looks at some great performances from the round, Benji Marshall's form, and the crazy weather from Monday night's clash.
Team List Tuesday - Analysis
SAM Bourke analyses all the NRL Team Lists released yesterday, looking at the ins and outs and Supercoach Studs and Duds.
LeagueUnlimited NYC Teams - 2015 Round 8
IT'S Teamlist Tuesday for Round 8 of the 2015 Holden Cup Under 20's Season! Around 5pm AEDT every Tuesday, the 16 teams for each NYC round will be posted right here!
The Synopsis - NRL Round 7
GEORGE Peterson gives us a rundown of all the action from what turned out to be an interesting weekend of Rugby League.
In the Spotlight - Round 8
GOOD day to you sir/madam.Round eight of In The Spotlight, comin' atcha.
Let's Talk Rep Round
WITH teams for the upcoming representative round to be named next Sunday, we shift our focus to the test match between Australia and the defending Four Nations champions, New Zealand and have a look at key selections looming for the City and Country teams.
LeagueUnlimited NRL Teams - 2015 Round 8
IT'S Teamlist Tuesday for Round 8 of the 2015 NRL Season! Around 5pm AEDT every Tuesday, the 16 teams for each NRL round will be posted right here!
Memorable Debuts - Round 8
ROB Crosby takes a look at the upcoming matches of the round and visits the archives to see which players debuted in the same game all those years ago.
Tuesday's Expert Wrap - NRL Round 7
TUESDAY'S Expert compiles all the scores and scorers from the weekend's NRL action, plus match details and player of the year points. Here's your look at Round 7!
Sharks take a bite out of Rabbitohs in cyclonic conditions
CRONULLA have recorded their third straight win, 18-10 in the wet and wild conditions of Shark Park with 3,978 fans braving the weather.
RESULTS: NYC Under 20's - 2015 Round 7
ALL the results from Round 7 of the 2015 National Youth Competition - the NRL Under 20's Holden Cup.
The Late Mail - Sharks v Rabbitohs
GET all the Late Mail ahead of tonight's clash between the Cronulla-Sutherland Sharks and the South Sydney Rabbitohs at Remondis Stadium.


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Lattice Design Oval Labels, 18 per sheet
Avery Pre-Designed Templates Microsoft Word
Oval labels add a touch of elegance to products, packages, boxes and bags. The distinctive shape also works for return address labels and gift tags.
Compatible Products:
22804, 22814, 22920, 22921, 80510
Free Offer! Avery Toolbar
The Avery Toolbar lets you get templates, tips and more--right from your web browser. Download it free today!


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Unloading a Muzzleloader
There are two ways to unload a muzzleloader.
- Unload a muzzleloader by discharging it into a suitable backstop. Do not fire into the air or into the ground at your feet in case the projectile ricochets.
- Use a CO2 discharger to clear the barrel.
- Percussion Lock Muzzleloaders: Slip the discharger over the nipple.
- Flintlock Muzzleloader: Place the discharger against the touchhole.
When a muzzleloader is unloaded, place your ramrod or loading rod in the barrel before leaning the firearm against a good rest—this will prevent debris from falling down the barrel and blocking the touchhole.


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Cor-Ten steel, 24' 10" x 10' 11" x 10' 11" (749.9 x 318.8 x 318.8 cm). Given anonymously. © 2006 Barnett Newman Foundation / Artists Rights Society (ARS), New York
Audio courtesy of Acoustiguide
If you are interested in reproducing images from The Museum of Modern Art web site, please visit the Image Permissions page (www.moma.org/permissions). For additional information about using content from MoMA.org, please visit About this Site (www.moma.org/site).
© Copyright 2011 The Museum of Modern Art


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Main Content
Order as many items as you like with our $4.99 flat rate shipping.
This item ships within one business day.
Order as many items as you like with our $4.99 flat rate shipping.
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You can't toast to your team with a warm drink! Keep your beverages perfectly frosty with this 2-pack of Kolder Holders. Each one is made of neoprene rubber to effectively insulate a 12oz. can or bottle; the outside displays your NBA squad's logo to satisfy your thirst for team spirit.
- 2-Pack of neoprene beverage holders
- Displays NBA team logo on side
- Full glued-in bottom
- Holds 12oz. can or bottle
- Insulates beverage and holds in condensation
- Made in China
- Officially licensed
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Special event items are produced by manufacturers only after the outcome of a game or event. These are advanced sale items and will ship immediately after they are received in our warehouse.
Manufacturer direct items are shipped directly from the manufacturer. These items are not available for international or expedited shipping.
Customized items can be personalized with options such as your name, your favorite number, and/or designs. Some options may be limited by league rules.


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Chicago Cutlery®Belmont™ 3-pc Knife Set
Chicago Cutlery®Belmont™ 3-pc Knife Set
In Stock
Product Actions
Additional Information
- Belmont™ 3-pc Knife Set includes 7-1/2" chef, 5" utility & 3-1/2" paring knives
- Professional stainless steel blades
- Sharpened for precision cutting
- Contoured soft grip handles for comfort
- Full Lifetime Warranty
Product Reviews
Chicago Cutlery® Warranty
Chicago Cutlery knife products (does not include cutting boards) are warranted to be free of defects in material and workmanship under normal household use for the lifetime of the product. Any piece found to be defective will be repaired or replaced at no charge with the same item or an item of equal or greater value. This warranty is not valid for products damaged by misuse, for purposes other than normal household use, or failure to follow the manufacturer's Use and Care instructions. In no event is World Kitchen, LLC liable for consequential damages.
Chicago Cutlery® Use & Care
Knife Care
For best results, hand-wash your knives with a soapy cloth and dry immediately. Soaking wood-handled knives in water can remove the natural oils from the handles. Dishwashing may cause nicks on the blade edges. Additionally, the heat and detergent may have a corrosive effect on the knives.
Sharpeners are not for use on scalloped or serrated edges. For optimum performance, knives should be sharpened after every couple of uses. Use a scouring powder to clean and remove metal particles from your sharpening steel. After cleaning the steel, rinse with water, dry it thoroughly and store in a dry place.
Sharpening Steel
- Hold sharpening steel point down on flat stable surface such as a table or cutting board.
- Angle knife blade approximately 15 degrees from the sharpening steel. Imagine the knife blade is at approximately 11 o'clock and 1 o'clock.
- Pull the knife down and across the sharpening steel in a slight arc, pulling the knife handle toward you.
- Repeat on the other side of the steel.
- Repeat these steps 3-5 times, alternating the right and left side of the cutting edge.
MagnaSharp® in Block sharpener
- Insert your fine edged knife into the sharpening slot.
- While applying slight downward pressure on the knife edge, pull the knife out of the slot.
- Repeat this 3-4 times, and your knife edge will be realigned and sharpened.
MagnaSharp® Mouse Sharpener
It is small enough to store in a drawer or, better yet, the back side is a magnet so you can place it on the refrigerator, your stove, or anywhere close to your cutlery.
- Open the sharpening area.
- Insert your fine edged knife into the sharpening slot.
- While applying slight downward pressure on the knife edge, pull the knife through.
- Repeat this 3-4 times, and your knife edge will be realigned and sharpened.
Sharp knives should never be stored loose in a drawer because contact with hard objects can dull the blade and reaching into a knife drawer can be very dangerous. Many Chicago Cutlery® sets are sold with a hardwood block for safe, convenient storage. MagnaStrip™ storage is another way for convenient and safe storage, saving counter space with a magnetic strip.
- Use the correct size and type of knife for the job.
- Cut away from the body when possible.
- Use knives with a wooden or polyethylene cutting board.
- Do not use a knife to stab, pull or lift materials.
- After handling a knife, lay it down in a cleared area with the blade away from the body and a safe distance from the edge of the cutting area.
- Do not reach blindly for a knife; reach deliberately for the handle.
- Never try to catch a falling knife.
1115583Chicago Cutlery® Belmont™ 6.5" Cleaver$19.99Description
Chicago Cutlery Belmont™ collection has professional high-carbon stainless steel blades with dual material handles. This collection is perfect for cooks that are looking to save time and are ready to take cooking to the next level.
1106301Chicago Cutlery® Belmont™ 2-pc Santoku / Paring Knife Set$22.99Description
These Chicago Cutlery® knives are strong, sharp and precise. Not to mention stylish, with their striking, striped handle. Use the Santoku knife for heavy-duty cutting jobs, the paring knife for smaller tasks. Not soft grip.
1119663Chicago Cutlery® Belmont™ 6.75" Santoku Knife$14.99Description
So what exactly is a Santoku knife? This Chicago Cutlery® Belmont™ Santoku knife has it all - strength, stability and style. Plus a reusable, blade-protecting knife sheath.
1120209Chicago Cutlery® Belmont™ 7.5" Chef Knife$14.99Description
You can earn your stripes in the kitchen by starting with this Belmont™ chef knife. Its full metal tang provides you the strength and stability you need - and a striking, striped handle for the style you want. And it includes a blade-protecting knife sheath that's reusable.
1106276$69.99 Was $119.99Chicago Cutlery® Belmont™ 16-pc Block Set$69.99 Was $119.99Description
If you're updating your outdated kitchen knives, why settle for second best? Choose this Belmont™ knife set. Chicago Cutlery® knives are known for their professional quality, precision sharpness and outstanding durability. The stainless steel blades are strong and resistant to rust, stains and pitting. And these Belmont™ knives have stylish, dual-material handles that you'll be proud to use - and to display.
1098733$5.59 Was $7.99Snapware® Snap 'N Stack® Food Storage Sandwich Box$5.59 Was $7.99Description
If you brown bag it, you'll love packing your lunch in this two-part stacking container. Use one section for your sandwich, the other for chips, salad, dessert. And if you're a lighter eater, just use one of the sections by itself. Prepack the containers, store them in your fridge or freezer, and you're good to go.
6010732Corelle® Livingware™ Winter Frost White 12.25" Serving Platter$10.99Description
Corelle® Livingware™... The original break and chip resistant glass dinnerware. Trust that it can stand up to the rigors of everyday life and still look great.
Functional and versatile, our Winter Frost White collection is a fundamental basic, perfect in its simplicity, and pure in its form.
1094283Chicago Cutlery® Essentials® 4-pc Steak Knife Set$14.99Description
Essentials collection has professional high-carbon stainless steel blades with black polymer handles. This collection is perfect for beginner cooks that are looking for simple cutting solutions at an everyday value.
5302525Pyrex® 2.5-qt Mixing Bowl$9.99Description
The Pyrex® 2-1/2-Quart Mixing Bowl is designed to make stirring and mixing quick and easy. The round shape gives you the space you need for full range stirring and is ideal for all of your cooking and baking needs.
1035985Corningware® French White® Pop-Ins® 20-oz Mug w/ Vented Lid$9.99Description
This mug has a vented lid specially designed for microwave use. The lid allows steam to escape, keeping your microwave clean and you safe from steam burns. The mug makes a great gift for a coworker or colleague.


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This article describes the work being done by scientists to determine the origin of water found in Earth's oceans. A supplemental exploration of the Herschel Space Observatory is included. The article is targeted to children ages 10-12.
This question is addressed through a series of questions and answers, each providing related introductory information such as how climate change is studied, the history of Earth's climate, and the effects of climate change on Earth's geology and... (View More) biology. The Climate Kids website is a NASA education resource featuring articles, videos, images and games focused on the science of climate change. (View Less)
Unit one of the "Carbon Connections: The Carbon Cycle and the Science of Climate" curriculum introduces the role of carbon (as carbon dioxide) as an atmospheric indicator. Students examine the impact of geologic and climatic history on current... (View More) climate by using computer models, measurements and the geologic record of past climate indicators. The unit contains five lessons entitled: Carbon Fizz, Carbon from the Past, Carbon Forcing, Global Connections, and Core Connections. Each of the five lessons includes focus questions, hands-on activities, virtual field trips, and interactive models. (View Less)
Materials Cost: 1 cent - $1 per group of students
In this self-paced tutorial, learners examine data to determine the relative contribution of what we call natural climate cycles and that of human-caused greenhouse gases to contemporary climate change. Changes in the Earth-Sun geometry over time... (View More) are explored using interactive digital applets. A section supporting pedagogical techniques that begin with student prior conceptions and a list of common Earth science student misconceptions are included. Vocabulary terms are hot linked to a glossary. This is the sixth of ten self-paced professional development modules providing opportunities for teachers to learn about climate change through first-hand data exploration. (View Less)
Materials Cost: Free per student
This textbook chapter introduces the buffalo as a keystone species, and describes the environmental impacts of its near extinction, including today's predominance of non-native species in the Great Plains. Human activities that contribute to... (View More) species extinction are addressed. Students graph historical sightings of buffalo, and calculate the number of buffalo killed for bone used in refining sugar and fertilizer and in the production of bone china. The resource includes a link to current news articles and a teacher's guide. This is the second chapter in the unit, Losing Biodiversity, examining the endangerment and extinction of entire species of plants and animals throughout the world due to human actions. The resource is part of Global System Science (GSS), an interdisciplinary course for high school students that emphasizes how scientists from a wide variety of fields work together to understand significant problems of global impact. (View Less)
Materials Cost: 1 cent - $1 per group of students
This introductory textbook chapter presents data demonstrating decreased global biodiversity and its link to human activity. The resource includes a field-based student investigation of local biodiversity, links to current news articles, and an... (View More) essay-based unit assessment. A teacher's guide supports classroom use. This is chapter 1 in the unit, Losing Biodiversity, is about the endangerment and extinction of entire species of plants and animals throughout the world due to human actions. The resource is part of Global System Science (GSS), an interdisciplinary course for high school students that emphasizes how scientists from a wide variety of fields work together to understand significant problems of global impact. (View Less)
Materials Cost: Free per student
This is a DVD about asteroids and impacts in the solar system. Learners can watch a 7-minute video of the "lifetime" of a meteor. The narrated, subtitled program includes images of impact craters on planets and asteroids, visualizations of the... (View More) Asteroid Belt, animations of collisions between asteroids, an explanation of how collisions between asteroids can create fragments that reach Earth as a meteorite, visualizations of resonances in the asteroid belt, the perturbation of an asteroid fragment toward Earth, an explanation of how meteors that impact Earth might have obtained high and low impact velocities, and visualizations of the range of outcomes from impacts by meteors with different velocities and sizes. The goal is to provide engaging and scientifically accurate animations and images of impact processes in the solar system. The program is specifically designed to dispel commonly-held misconceptions and improve general understanding of solar system science among student's grades 5-12, as well as a broad lay audience. In addition to the 7-minute stand-alone video, the DVD also contains two interactives for Windows® and Macintosh® computers. The first interactive is a version of the above program that allows students and other users to view segments in any order through answering some of the most-commonly asked questions about asteroid impacts. The second interactive, "Make a Collision," allows users to simulate asteroid collisions, by selecting the parameters of collisions between asteroids and then seeing the results. The third interactive, "ImpactChallenge," provides additional experience with simulations Asteroid Belt impacts by giving users additional parameters that can be adjusted to make a wider variety of asteroid collisions. (View Less)
In this problem set, learners will analyze a table of the length of day (hours) and the number of days per year on Earth in past eras. They will calculate future values, plot some of the data and identify the rate of increase. Answer key is... (View More) provided. This is part of Earth Math: A Brief Mathematical Guide to Earth Science and Climate Change. (View Less)
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This activity is designed to introduce students to planetary geologic features and processes. First, students will use NASA satellite images to identify geologic surface features on the "Blue Marble" (Earth), and will explore the connection between... (View More) those features and the geologic processes that created them. Using that information, students will then compare and discuss similar features on images from other planets. Included are the following materials: teacher's guide (with reference and resource information), student's guide (with activity sheets), and multiple cards of planetary images. Note that the range of targeted grade levels is quite broad; however, explicit adaptations for younger students are highlighted throughout the teacher's guide. This lesson is part of the Expedition Earth and Beyond Education Program. (View Less)
Materials Cost: $1 - $5 per group of students
In this activity, students investigate sea level change during glacial maxima during the Ice Ages, and learn how lowered sea level presented additional routes for intercontinental human migration. Summary background information, data and images... (View More) supporting the activity are available on the Earth Update data site. To complete the activity, students will need to access the Space Update multimedia collection, which is available for download and purchase for use in the classroom. (View Less)
Materials Cost: Free per student


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There are finally some official cast pics for "Tiny Tonight" and the ladies are looking fab!
With a week to go until the premiere of "Tiny Tonight," VH1 has unveiled some color art for the show which will debut with a year-end review of all things pop culture.
Tiny will be discussing politics, fashion, celebrities and entertainment with Tamar Braxton, Claudia Jordan and Trina. "Tiny Tonight" debuts December 17 at 10 p.m. on VH1. Check out the cast pics below!
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Just because she's a rookie at marriage (and divorce) doesn't mean she can't give great advice. Porsha Stewart recently spoke to Sister 2 Sister Publisher Jamie Foster Brown and gave a little insight into what the key to a successful marriage is.
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Get more from Porsha in the October 2013 issue of Sister 2 Sister.
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Big gains await developing countries if they raise their energy productivity, research by the McKinsey Global Institute (MGI) has found: they could slow the growth of their energy demand by more than half over the next 12 years—to 1.4 percent a year, from 3.4—which would leave demand some 25 percent lower in 2020 than it would otherwise have been (Exhibit 1). That is a reduction larger than total energy consumption in China today.
Policy makers and businesses in developing regions must not be deterred from boosting energy productivity (the output they achieve from the energy they consume) because of the present weakening economic environment and falling oil prices; these do not affect the long-term projections in the study.1 1.
The study—conducted before the economic slowdown in late 2008—assumes, among other things, global GDP growth of 3.2 percent annually to 2020 (including, for example, 6.4 percent annual growth in China) and an average oil price of $50 a barrel. A fresh review of the data and underlying assumptions indicates that slowing worldwide economic growth in the near term will have minimal effects on the long-term projections in this article. Time is of the essence: developing economies will install half or more of the capital stock that will be in place in 2020 between now and then. Every building or industrial plant constructed without optimal energy efficiency represents a lost opportunity to lock in lower energy consumption for decades.
Developing countries could cut energy demand growth by more than half through higher energy productivity.
Just by using existing technologies that would pay for themselves in future energy savings, consumers and businesses could save some $600 billion a year by 2020. Companies that pioneer energy efficiency in their home markets will be well placed to carve out a leading position in the global market for "green" products and services before it matures. Indeed, 65 percent of available positive-return opportunities to boost energy productivity are located in developing regions (Exhibit 2).
Developing regions represent 65 percent of the positive-return opportunities to reduce energy demand.
The benefits of higher energy efficiency are achievable with an investment of $90 billion annually over the next 12 years—only about half of what these economies would otherwise need to spend on their energy supply infrastructure to keep pace with higher consumption. Indeed, because of lower labor costs, the price tag for investing in energy productivity is on average 35 percent lower in developing economies than in advanced ones.
At present, a range of market failures and information barriers discourage developing countries from increasing their energy productivity, even with high energy prices. Capital constraints, particularly for low-income households, are a major hurdle. Consumers also tend to lack the information they need to make the right choices. Many companies, insulated from the true price of energy, have relatively little incentive to identify and invest in the fragmented energy savings opportunities that are available. And today's tighter credit markets are squeezing the financing of all investments—even less risky ones, such as those in energy efficiency.
MGI calculates that somewhat more than half of the current variation in energy productivity among developing countries can be explained by climate, industry structure, and energy policies (Exhibit 3). Climatic extremes that require the use of heating and cooling systems unavoidably increase energy consumption in relation to GDP in some regions. Heavy industrialization is a consideration because countries with large manufacturing sectors tend to consume more energy and have lower energy productivity. But for energy policy, there are adjustments that developing countries can make. MGI identifies four priority areas.
Energy policies, climate, and industry structure explain somewhat more than half of the energy productivity variation among developing countries.
The first is to reduce energy subsidies, as they tend to lower energy productivity. The International Energy Agency (IEA) estimates that in 2005, these subsidies totaled more than $250 billion a year in developing countries—more than the annual investment needed to build their electricity supply infrastructure. Protecting the poor from the stress of high energy prices is a legitimate goal. But there are other ways to achieve this and similar welfare goals at a lower cost. For example, in Latin America and elsewhere, governments have tried to reduce poverty by using conditional cash-transfer programs, which can also help compensate low-income households for high energy costs. To ease the transition to more efficient energy use, governments should consider providing finance for upgrades to more efficient equipment and use some of the savings from lower energy consumption to assist poor segments of the population.
Second, governments should provide incentives for utilities to improve energy efficiency and encourage their customers to do the same. Policy options include revenue incentives and certification programs that measure and reward progress toward achieving efficiency targets and also encourage the adoption of technologies such as smart metering that help households better manage their energy use.
Implementing and enforcing energy efficiency standards is a third area for action. Such standards boost production of more efficient appliances and equipment and reduce their cost. Indonesia has recently adopted the UN technical regulation on auto energy efficiency, for example, and Ghana has pioneered standards for household appliances in Africa.
A fourth priority is encouraging public–private partnerships, such as collaborations between governments, energy service companies, utilities, and mortgage companies, to finance higher energy efficiency in buildings. China, which manufactures 70 percent of the world's lightbulbs, now has very large subsidies in place to promote the uptake of energy-efficient bulbs.
If developing countries and their businesses seize the initiative on energy productivity, they will cut their energy costs, insulate themselves from future energy shocks, and secure a more sustainable development path—benefits that are all the more desirable given the current global financial turmoil.
This article is based on the McKinsey Global Institute report Fueling sustainable development: The energy productivity solution.
Diana Farrell is the deputy director of the National Economic Council and deputy economic advisor to President Barack Obama. When this report was written, she was director of the McKinsey Global Institute, where Jaana Remes is a consultant.
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GFF Parsing
(→Writing GFF3)
(→Writing GFF3 from scratch)
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|Line 237:
out_file = "your_file.gff"
out_file = "your_file.gff"
seq = Seq("
seq = Seq("")
rec = SeqRecord(seq, "ID1")
rec = SeqRecord(seq, "ID1")
qualifiers = {"source": "prediction", "score": 10.0, "other": ["Some", "annotations"],
qualifiers = {"source": "prediction", "score": 10.0, "other": ["Some", "annotations"],
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##gff-version 3
##gff-version 3
ID1 prediction gene 1 20 10.0 + . other=Some,annotations;ID=gene1
ID1 prediction gene 1 20 10.0 + . other=Some,annotations;ID=gene1
ID1 prediction exon 1 5 . + . Parent=gene1
ID1 prediction exon 1 5 . + . Parent=gene1
Revision as of 19:26, 9 April 2011
GFF Parsing
Note: GFF parsing is not yet integrated into Biopython. This documentation is work towards making it ready for inclusion. You can retrieve the current version of the GFF parser from: http://github.com/chapmanb/bcbb/tree/master/gff. Comments are very welcome.
Generic Feature Format (GFF) is a biological sequence file format for representing features and annotations on sequences. It is a tab delimited format, making it accessible to biologists and editable in text editors and spreadsheet programs. It is also well defined and can be parsed via automated programs. GFF files are available from many of the large sequencing and annotation centers. The specification provides full details on the format and its uses.
Biopython provides a full featured GFF parser which will handle several versions of GFF: GFF3, GFF2, and GTF. It supports writing GFF3, the latest version.
GFF parsing differs from parsing other file formats like GenBank or PDB in that it is not record oriented. In a GenBank file, sequences are broken into discrete parts which can be parsed as a whole. In contrast, GFF is a line oriented format with support for nesting features. GFF is also commonly used to store only biological features, and not the primary sequence.
These differences have some consequences in how you will deal with GFF:
- Files are first examined to determine available annotations and define items of interest.
- Sequences will often be parsed separately, from an associated FASTA file.
- Parsing needs to consider available memory, which can be quickly used up on files with many annotations. This problem can be solved via two methods:
- Limiting parsing to features of interest.
- Iterating over portions of the file.
The documentation below provides a practical guide to examining, parsing and writing GFF files in Python.
Examining your GFF file
Since GFF is a very general format, it is extremely useful to start by getting a sense of the type of data in the file and how it is structured. GFFExaminer provides an interface to examine and query the file. To examine relationships between features, examine a dictionary mapping parent to child features:
import pprint from BCBio.GFF import GFFExaminer in_file = "your_file.gff" examiner = GFFExaminer() in_handle = open(in_file) pprint.pprint(examiner.parent_child_map(in_handle)) in_handle.close()
This file contains a flexible three level description of coding sequences: genes have mRNA trascripts; those mRNA transcripts each contain common features of coding sequence, the CDS itself, exon, intron and 5' and 3' untranslated regions. This is a common GFF structure allowing representation of multiple transcripts:
{('Coding_transcript', 'gene'): [('Coding_transcript', 'mRNA')], ('Coding_transcript', 'mRNA'): [('Coding_transcript', 'CDS'), ('Coding_transcript', 'exon'), ('Coding_transcript', 'five_prime_UTR'), ('Coding_transcript', 'intron'), ('Coding_transcript', 'three_prime_UTR')]}
Another item of interest for designing your parse strategy is understanding the various tags used to label the features. These consist of:
- gff_id -- The record identifier being described. This will often refer to a chromosome or other scaffold sequence.
- gff_source -- The source description from the second column of the GFF file, which specifies how a feature was generated.
- gff_type -- The type of the feature, pulled from the 3rd column of the GFF file.
- gff_source_type -- All combinations of sources and types in the file.
The available_limits function in the examiner gives you a high level summary of these feature attributes, along with counts for the number of times they appear in the file:
import pprint from BCBio.GFF import GFFExaminer in_file = "your_file.gff" examiner = GFFExaminer() in_handle = open(in_file) pprint.pprint(examiner.available_limits(in_handle)) in_handle.close()
{'gff_id': {('I',): 159, ('II',): 3, ('III',): 2, ('IV',): 5, ('V',): 2, ('X',): 6}, 'gff_source': {('Allele',): 1, ('Coding_transcript',): 102, ('Expr_profile',): 1, ('GenePair_STS',): 8, ('Oligo_set',): 1, ('Orfeome',): 8, ('Promoterome',): 5, ('SAGE_tag',): 1, ('SAGE_tag_most_three_prime',): 1, ('SAGE_tag_unambiguously_mapped',): 12, ('history',): 30, ('mass_spec_genome',): 7}, 'gff_source_type': {('Allele', 'SNP'): 1, ('Coding_transcript', 'CDS'): 27, ('Coding_transcript', 'exon'): 33, ('Coding_transcript', 'five_prime_UTR'): 4, ('Coding_transcript', 'gene'): 2, ('Coding_transcript', 'intron'): 29, ('Coding_transcript', 'mRNA'): 4, ('Coding_transcript', 'three_prime_UTR'): 3, ('Expr_profile', 'experimental_result_region'): 1, ('GenePair_STS', 'PCR_product'): 8, ('Oligo_set', 'reagent'): 1, ('Orfeome', 'PCR_product'): 8, ('Promoterome', 'PCR_product'): 5, ('SAGE_tag', 'SAGE_tag'): 1, ('SAGE_tag_most_three_prime', 'SAGE_tag'): 1, ('SAGE_tag_unambiguously_mapped', 'SAGE_tag'): 12, ('history', 'CDS'): 30, ('mass_spec_genome', 'translated_nucleotide_match'): 7}, 'gff_type': {('CDS',): 57, ('PCR_product',): 21, ('SAGE_tag',): 14, ('SNP',): 1, ('exon',): 33, ('experimental_result_region',): 1, ('five_prime_UTR',): 4, ('gene',): 2, ('intron',): 29, ('mRNA',): 4, ('reagent',): 1, ('three_prime_UTR',): 3, ('translated_nucleotide_match',): 7}}
GFF Parsing
Basic GFF parsing
Generally, the GFF parser works similar to other parsers in Biopython. Calling parse with a handle to a GFF file returns a set of SeqRecord objects corresponding to the various IDs referenced in the file:
from BCBio import GFF in_file = "your_file.gff" in_handle = open(in_file) for rec in GFF.parse(in_handle): print rec in_handle.close()
The rec object is a Biopython SeqRecord containing the features described in the GFF file. The features are ordered into parent-child relationships based on the line by line information in the original GFF file. See the detailed documentation on SeqRecord and SeqFeature objects for more details on accessing the information in these objects.
Since a GFF file is not broken down into an explicit record structure, this requires reading the entire file, parsing all of the features, and then returning those as records. This will be fine for small files, but for most real life cases you will want to restrict parsing to a set of features of interest or a section of lines at once to conserve memory.
Limiting to features of interest
A GFF file will commonly contain many types of features, and you will be interested in retrieving a subset of these. The limit_info argument to GFF.parse allows exact specification of which features to parse, turn into objects and retrieve. An example is retrieving all coding sequence on chromosome 1:
from BCBio import GFF in_file = "your_file.gff" limit_info = dict( gff_id = ["chr1"], gff_source = ["Coding_transcript"]) in_handle = open(in_file) for rec in GFF.parse(in_handle, limit_info=limit_info): print rec.features[0] in_handle.close()
You will get back a single record for chromosome 1 which contains all of the coding features in memory for further manipulation. Depending on your memory requirements and workflow, it may make sense to do analysis over each chromosome or set of features you are interested in.
Iterating over portions of a file
Another way to break up a large GFF file parse into sections is to limit the number of lines that are read at once. This is a useful workflow for GFF files in which you don't need all of the features at once and can do something useful with a few at a time. To do this, pass the target_lines argument to GFF.parse:
from BCBio import GFF in_file = "your_file.gff" in_handle = open(in_file) for rec in GFF.parse(in_handle, target_lines=1000): print rec in_handle.close()
The parser will attempt to smartly break up the file at your requested number of lines. For instance, if 1000 lines happens to come in the middle of a nested coding feature (gene -> transcript -> CDS/exon/intron), the parser would continue until the entire feature region is read. This helps ensure that you have fully formed features for analysis.
If your file has no nesting of features, or you just want a single line at once, you can set target_lines=1 and the parser will happily give you back and SeqRecord object with a single SeqFeature for every line.
Providing initial sequence records
from BCBio import GFF from Bio import SeqIO in_seq_file = "seqs.fa" in_seq_handle = open(in_seq_file) seq_dict = SeqIO.to_dict(SeqIO.parse(in_seq_handle, "fasta")) in_seq_handle.close() in_file = "your_file.gff" in_handle = open(in_file) for rec in GFF.parse(in_handle, base_dict=seq_dict): print rec in_handle.close()
Writing GFF3
GFF3Writer takes an iterator of SeqRecord objects, and writes
each SeqFeature as a GFF3 line:
- seqid -- SeqRecord ID
- source -- Feature qualifier with key "source"
- type -- Feature type attribute
- start, end -- The Feature Location
- score -- Feature qualifier with key "score"
- strand -- Feature strand attribute
- phase -- Feature qualifier with key "phase"
The remaining qualifiers are the final key/value pairs of the attribute.
A feature hierarchy is represented as sub_features of the parent feature. This handles any arbitrarily deep nesting of parent and child features.
Converting other formats to GFF3
from BCBio import GFF from Bio import SeqIO in_file = "your_file.gb" out_file = "your_file.gff" in_handle = open(in_file) out_handle = open(out_file, "w") GFF.write(SeqIO.parse(in_handle, "genbank"), out_handle) in_handle.close() out_handle.close()
Writing GFF3 from scratch
You can create Biopython SeqRecord and SeqFeature objects from scratch and use these to generate GFF output. Chapter 4 of the Tutorial goes into detail about the objects, and this example demonstrates the major features:
from BCBio import GFF from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio.SeqFeature import SeqFeature, FeatureLocation out_file = "your_file.gff" seq = Seq(""GATCGATCGATCGATCGATC) rec = SeqRecord(seq, "ID1") qualifiers = {"source": "prediction", "score": 10.0, "other": ["Some", "annotations"], "ID": "gene1"} sub_qualifiers = {"source": "prediction"} top_feature = SeqFeature(FeatureLocation(0, 20), type="gene", strand=1, qualifiers=qualifiers) top_feature.sub_features = [SeqFeature(FeatureLocation(0, 5), type="exon", strand=1, qualifiers=sub_qualifiers), SeqFeature(FeatureLocation(15, 20), type="exon", strand=1, qualifiers=sub_qualifiers)] rec.features = [top_feature] with open(out_file, "w") as out_handle: GFF.write([rec], out_handle)
This generates the following GFF:
##gff-version 3 ##sequence-region ID1 1 20 ID1 prediction gene 1 20 10.0 + . other=Some,annotations;ID=gene1 ID1 prediction exon 1 5 . + . Parent=gene1 ID1 prediction exon 16 20 . + . Parent=gene1