Metadata Federation of PICES Member Countries

(Document pdf contains 193 pages) Executive Summary (pdf, < 0.1 Mb) 1. Introduction (pdf, 0.2 Mb) 1.1 Data sharing, international boundaries and large marine ecosystems 2. Objectives (pdf, 0.3 Mb) 3. Background (pdf, < 0.1 Mb) 3.1 North Pacific Ecosystem Metadatabase 3.2 First federation effort: NPEM and the Korea Oceanographic Data Center 3.2 Continuing effort: Adding Japan’s Marine Information Research Center 4. Metadata Standards (pdf, < 0.1 Mb) 4.1 Directory Interchange Format 4.2 Ecological Metadata Language 4.3 Dublin Core 4.3.1. Elements of DC 4.4 Federal Geographic Data Committee 4.5 The ISO 19115 Metadata Standard 4.6 Metadata stylesheets 4.7 Crosswalks 4.8 Tools for creating metadata 5. Communication Protocols (pdf, < 0.1 Mb) 5.1 Z39.50 5.1.1. What does Z39.50 do? 5.1.2. Isite 6. Clearinghouses (pdf, < 0.1 Mb) 7. Methodology (pdf, 0.2 Mb) 7.1 FGDC metadata 7.1.1. Main sections 7.1.2. Supporting sections 7.1.3. Metadata validation 7.2 Getting a copy of Isite 7.3 NSDI Clearinghouse 8. Server Configuration and Technical Issues (pdf, 0.4 Mb) 8.1 Hardware recommendations 8.2 Operating system – Red Hat Linux Fedora 8.3 Web services – Apache HTTP Server version 2.2.3 8.4 Create and validate FGDC-compliant Metadata in XML format 8.5 Obtaining, installing and configuring Isite for UNIX/Linux 8.5.1. Download the appropriate Isite software 8.5.2. Untar the file 8.5.3. Name your database 8.5.4. The zserver.ini file 8.5.5. The sapi.ini file 8.5.6. Indexing metadata 8.5.7. Start the Clearinghouse Server process 8.5.8. Testing the zserver installation 8.6 Registering with NSDI Clearinghouse 8.7 Security issues 9. Search Tutorial and Examples (pdf, 1 Mb) 9.1 Legacy NSDI Clearinghouse search interface 9.2 New GeoNetwork search interface 10. Challenges (pdf, < 0.1 Mb) 11. Emerging Standards (pdf, < 0.1 Mb) 12. Future Activity (pdf, < 0.1 Mb) 13. Acknowledgments (pdf, < 0.1 Mb) 14. References (pdf, < 0.1 Mb) 15. Acronyms (pdf, < 0.1 Mb) 16. Appendices 16.1. KODC-NPEM meeting agendas and minutes (pdf, < 0.1 Mb) 16.1.1. Seattle meeting agenda, August 22–23, 2005 16.1.2. Seattle meeting minutes, August 22–23, 2005 16.1.3. Busan meeting agenda, October 10–11, 2005 16.1.4. Busan meeting minutes, October 10–11, 2005 16.2. MIRC-NPEM meeting agendas and minutes (pdf, < 0.1 Mb) 16.2.1. Seattle Meeting agenda, August 14-15, 2006 16.2.2. Seattle meeting minutes, August 14–15, 2006 16.2.3. Tokyo meeting agenda, October 19–20, 2006 16.2.4. Tokyo, meeting minutes, October 19–20, 2006 16.3. XML stylesheet conversion crosswalks (pdf, < 0.1 Mb) 16.3.1. FGDCI to DIF stylesheet converter 16.3.2. DIF to FGDCI stylesheet converter 16.3.3. String-modified stylesheet 16.4. FGDC Metadata Standard (pdf, 0.1 Mb) 16.4.1. Overall structure 16.4.2. Section 1: Identification information 16.4.3. Section 2: Data quality information 16.4.4. Section 3: Spatial data organization information 16.4.5. Section 4: Spatial reference information 16.4.6. Section 5: Entity and attribute information 16.4.7. Section 6: Distribution information 16.4.8. Section 7: Metadata reference information 16.4.9. Sections 8, 9 and 10: Citation information, time period information, and contact information 16.5. Images of the Isite server directory structure and the files contained in each subdirectory after Isite installation (pdf, 0.2 Mb) 16.6 Listing of NPEM’s Isite configuration files (pdf, < 0.1 Mb) 16.6.1. zserver.ini 16.6.2. sapi.ini 16.7 Java program to extract records from the NPEM metadatabase and write one XML file for each record (pdf, < 0.1 Mb) 16.8 Java program to execute the metadata extraction program (pdf, < 0.1 Mb) A1 Addendum 1: Instructions for Isite for Windows (pdf, 0.6 Mb) A2 Addendum 2: Instructions for Isite for Windows ADHOST (pdf, 0.3 Mb)

The BACOMA cod-end. History and recent developments in BACOMA cod-end regulations and a proposal for abetter specification of the BACOMA cod-end for Baltic Sea cod fishery

To improve the cod stocks in the Baltic Sea, a number of regulations have recently been established by the International Baltic Sea Fisheries Commission (IBSFC) and the European Commission. According to these, fishermen are obliged to use nets with escape windows (BACOMA nets) with a mesh size of the escape window of 120 mm until end of September 2003. These nets however, retain only fish much larger than the legal minimum landing size would al-low. Due to the present stock structure only few of such large fish are however existent. As a consequence fishermen use a legal alternative net. This is a conventional trawl with a cod-end of 130 mm diamond-shaped meshes (IBSFC-rules of 1st April 2002), to be increased to 140 mm on 1st September 2003, according to the mentioned IBSFC-rule. Due legal alterations of the net by the fishermen (e.g. use of extra stiff net material) these nets have acquired extremely low selective properties, i. e. they catch very small fish and produce great amounts of discards. Due to the increase of the minimum landing size from 35 to 38 cm for cod in the Baltic, the amount of discards has even increased since the beginning of 2003. Experiments have now been carried out with the BACOMAnet on German and Swedish commercial and research vessels since arguments were brought forward that the BACOMA net was not yet sufficiently tested on commercial vessels. The results of all experiments conducted so far, are compiled and evaluated here. As a result of the Swedish, Danish and German initiative and research the European Commission reacted upon this in June 2003 and rejected the increase of the diamond-meshed non-BACOMA net from 130 mm to 140mm in September 2003. To protect the cod stocks in the Baltic Sea more effectively the use of traditional diamond meshed cod-ends with-out escape window are prohibited in community waters without derogation, becoming effective 1st of September 2003. To enable more effective and simplified control of the bottom trawl fishery in the Baltic Sea the principle of a ”One-Net-Rule“ is enforced. This is going to be the BACOMA net, with the meshes of the escape window being 110 mm for the time being. The description of the BACOMA net as given in the IBSFC-rules no.10 (revision of the 28th session, Berlin 2002) concentrates on the cod-end and the escape window but only to a less extent on the design and mesh-composition of the remaining parts of the net, such as belly and funnel and many details. Thus, the present description is not complete and leaves, according to fishermen, ample opportunity for manipulation. An initiative has been started in Germany with joint effort from scientists and the fishery to better describe the entire net and to produce a proposal for a more comprehensive description, leaving less space for manipulation. A proposal in this direction is given here and shall be seen as a starting point for a discussion and development towards an internationally uniform net, which is agreed amongst the fishery, scientists and politicians. The Baltic Sea fishery is invited to comment on this proposal, and recommendations for further improvement and specifications are welcomed. Once the design is agreed by the Baltic Fishermen Association, it shall be proposed to the IBSFC and European Commission via the Baltic Fishermen Association.

Ostseedorschselektion - bestehende und vorgesehene neue technische Maßnahmen

Since the beginning of the nineties the situation of the Baltic cod stock is deteriorating constantly. The fishery administration (International Baltic Sea Fisheries Commission) tries to counter this by issuing new technical measures. Existing measures (raise of mesh opening from 105 to 120 mm, “Danish” and “Swedish” escape windows) and newly introduced technical measures (BACOMA codend and raise of the mesh opening in conventional codends to 130 mm) show a number of deficiencies putting their efficiency in doubt. Available well tested alternatives to the newly introduced measures without their negative side effects (codends made of netting turned by 90°, and other designs) are presently left out of regard. Models of socioeconomic effects are likewise ignored.

Neues aus der Selektionsforschung am Ostseedorsch

In account of the decision of the IBSFC (International Baltic Sea Fisheries Commission) to admit alternative codend constructions to the presently legal of diamond meshes with 120 mm mesh opening, since seven years a vivid research activity is encouraged at the fishing technology institutions around the Baltic. Though a center of gravity in this field of research lies in the EUproject BACOMA (participants Finland Sweden, Denmark) also the corresponding national institutes of other Baltic countries (Germany, Poland, Russia) have been active with similar investigations. German experiments in 1999 dealt with the effect of the use of netting made of double instead of single yarn on the selectivity. Further research was done on modifications of codends made from netting turned 90° from its original orientation and on simplified versions of the so-called Multipanel codend which consists of three equal diamond and three square mesh panels. The experiments demonstrated on the one hand a definite deterioration of the selective properties in a codend made from double instead of single yarn. Constructional changes in codends made from netting turned 90° on the other hand brought a further improvement of the selectivity of such codends. Finally, the investigations on the Multipanel codend revealed the overwhelming influence of the square mesh panels on the selectivity success. If in a conventional diamond codend three windows are cut out starting 50 cm from the real end of the codend in such a way that the remaining parts have the same breadth as the square mesh panels to insert, the selective effect of such a codend is remarkably improved. According to further preliminary tests this seems to be nearly independent from the type of material used.

Abundance of harbor porpoise (Phocoena phocoena) in three Alaskan regions, corrected for observer errors due to perception bias and species misidentification, and corrected for animals submerged from view

Estimating the abundance of cetaceans from aerial survey data requires careful attention to survey design and analysis. Once an aerial observer perceives a marine mammal or group of marine mammals, he or she has only a few seconds to identify and enumerate the individuals sighted, as well as to determine the distance to the sighting and record this information. In line-transect survey analyses, it is assumed that the observer has correctly identified and enumerated the group or individual. We describe methods used to test this assumption and how survey data should be adjusted to account for observer errors. Harbor porpoises (Phocoena phocoena) were censused during aerial surveys in the summer of 1997 in Southeast Alaska (9844 km survey effort), in the summer of 1998 in the Gulf of Alaska (10,127 km), and in the summer of 1999 in the Bering Sea (7849 km). Sightings of harbor porpoise during a beluga whale (Phocoena phocoena) survey in 1998 (1355 km) provided data on harbor porpoise abundance in Cook Inlet for the Gulf of Alaska stock. Sightings by primary observers at side windows were compared to an independent observer at a belly window to estimate the probability of misidentification, underestimation of group size, and the probability that porpoise on the surface at the trackline were missed (perception bias, g(0)). There were 129, 96, and 201 sightings of harbor porpoises in the three stock areas, respectively. Both g(0) and effective strip width (the realized width of the survey track) depended on survey year, and g(0) also depended on the visibility reported by observers. Harbor porpoise abundance in 1997–99 was estimated at 11,146 animals for the Southeast Alaska stock, 31,046 animals for the Gulf of Alaska stock, and 48,515 animals for the Bering Sea stock.

Fish production, catches and the carrying capacity of the world oceans

A brief review of the status of the world fisheries is presented with emphasis on the differences between catches (= landings + bycatch), biological production of fish, and predation (= production - catches). The ECOPATH II approach implemented as a new, Windows-based software is then shown to allow construction of a stratified world model accoutinng for global catches, production of and predation on fishes, and thus improved estimates of global potentials. A newly initiated, cooperative project is described through which the foundation for such a global model could be constructed, based on a stratified database with more than 100 trophic models. Collaborators are invited to join in this, and will be assisted in constructing models covering their areas of interest.

Ecological modeling for all

A brief review of the status of the ECOPATH modeling approach and software is presented, with emphasis on the recent release of a Windows version (ECOPATH 3.0), which enables consideration of uncertainties, and sets the stage for simulation modeling using ECOSIM. Modeling of coral reefs is emphasized.

History of a Systematics Odyssey: The Marine Flora and Fauna of the Eastern United States

On an early fall day in September 1962 I sat quietly, thoughtfully, at my large desk in a newly renovated corner office in the old Crane wing of the Lillie Building, Marine Biological Laboratory (MBL), Woods Hole, Massachusetts. Looking out through high, ancient windows, I could see the busy main street of Woods Hole in the foreground, Martha's Vineyard beyond, behind me the MBL Stone Candle House, across the street the Woods Hole Oceanographic Institution (WHOI) and to the far right, the Biological Laboratory of the Bureau of Commercial Fisheries (BCF)(Fig. 1). Down the inner hall from my office stretched renovated quarters for the fledgling, ongoing, year-round MBL Systematics-Ecology Program (SEP), which I had been invited to direct.

Equatorial upwelling at Galapagos: the cadmium record in corals since 1600 [abstract and figures]

EXTRACT (SEE PDF FOR FULL ABSTRACT): Chemical isolation of lattice-bound trace elements in marine carbonates has opened new windows to paleoceanographic study. In a modern context at the Galapagos Islands, oceanic upwelling variability is mirrored by changes in the Cd content of reef-building corals. This association derives from cadmium's nutrient-like distribution in the water column and its ability to substitute for calcium in the aragonite lattice of corals. Given corals of sufficient age, it is thus possible to reconstruct near-term ENSO-related changes in surface waters of the eastern Equatorial Pacific on annual and sub-annual timescales.

In utero domoic acid toxicity: a fetal basis to adult disease in the California sea lion (Zalophus californianus)

California sea lions have been a repeated subject of investigation for early life toxicity, which has been documented to occur with increasing frequency from late February through mid-May in association with organochlorine (PCB and DDT) poisoning and infectious disease in the 1970's and domoic acid poisoning in the last decade. The mass early life mortality events result from the concentrated breeding grounds and synchronization of reproduction over a 28 day post partum estrus cycle and 11 month in utero phase. This physiological synchronization is triggered by a decreasing photoperiod of 11.48 h/day that occurs approximately 90 days after conception at the major California breeding grounds. The photoperiod trigger activates implantation of embryos to proceed with development for the next 242 days until birth. Embryonic diapause is a selectable trait thought to optimize timing for food utilization and male migratory patterns; yet from the toxicological perspective presented here also serves to synchronize developmental toxicity of pulsed environmental events such as domoic acid poisoning. Research studies in laboratory animals have defined age-dependent neurotoxic effects during development and windows of susceptibility to domoic acid exposure. This review will evaluate experimental domoic acid neurotoxicity in developing rodents and, aided by comparative allometric projections, will analyze potential prenatal toxicity and exposure susceptibility in the California sea lion. This analysis should provide a useful tool to forecast fetal toxicity and understand the impact of fetal toxicity on adult disease of the California sea lion.

The software for oceanographic data management: VODC for PC 2.0

To manage and process a large amount of oceanographic data, users must have powerful tools that simplify these tasks. The VODC for PC is software designed to assist in managing oceanographic data. It based on 32 bits Windows operation system and used Microsoft Access database management system. With VODC for PC users can update data simply, convert to some international data formats, combine some VODC databases to one, calculate average, min, max fields for some types of data, check for valid data…

Effects of Zataria multiflora Boiss essential oil and nisin on the growth of Staphylococcus aureus in light salted silver carp fillet (Hypophthalmichthys molitrix)

There is an increasing demand in developing newer and safer methods in preserving food products.Among which herbal additives seem to attract evermore attention recently.the major advantage of herbal additives is due to their favorable aroma besides their antimicrobial effects and less expensive than chemical additives. Zataria multiflora Boiss is a native Iranian herb which is used vastly as a food preserver essential oils and also medical usage. Metabolites of harmless bacteria, such as Nisin are also known to be safe preservatives that have antimicrobial activity. However to establish the usefulness of natural antimicrobial preservatives, they must be evaluated alone and in combination with other preservation factors to determine whether there are synergistic effects in rigid media . In this study were evaluated the effects of different concentrations of Zataria multiflora (EO 0, 0.005, 0.015, 0.045, 0.135, 0.405 ,0.810 %) and Nisin(0, 0.15, 0.25, 0.75 μg/ml) and Storage time (up to 21 days) on growth of Staphylococcus aureus ATCC 6538 in a food model system(light salted fish of silver carp, Hypophthalmichthys molitrix). The results on growth of S. aureus were evaluated using SPSS 15.0 statistical software (SPSS 15.0 for windows, SPSS Inc.) and analyzed the logarithm of total count of the bacteria by Tukey Test. Results were considered statistically significant when P≤0.05. The growth of Staphylococcus aureus was affected significantly(P<0.05) by EO and Nisin and also combinations of EO and Nisin. Samples treated with 0.135, 0.405 and 0.810% of thyme essential oil showed a significant decrease on the growth of the bacteria compared with an treated samples(P<0.05). No significant difference was seen on the growth of S.aureus in samples treated with lower concentrations of Z.multiflora(below 0.045%) and untreated group(P>0.05). The most inhibitory effects were seen in samples treated with 0.405% and 0.810% of thyme essential oil until 9 and 12 days after storage,respectively. Also there was significant inhibtory effect(P<0.05) in different concentration of nisin on the organism compared with an treated samples. The synergism effects of the Eo and nisin on the growth rate of the bacteria was significant (P<0.05) compared with untreated samples and samples treated with the Eo or nisin, only. Synergismic effects was observed at concentration of 0.405 and 0.810% of Z. multiflora essential oil with 0.25 μg/ml Nisin, respectively until 15 days after storage. As expected it is preferred to apply the least possible amounts of additives in food preserving that not only are effective and safe but are economically justifiable.